Source assessment, 2026-10-24. No publication quotations are added. Full original access, selected sections actually read, target-data checks, and independent corroboration are distinguished below. A saved HTTP response, cache flag or successful download is not treated as proof of scientific reading.
Access: operative original. OCR of original pp. 6483–6486, Methods, Results, Figures 3–5 captions.
Human HeLa TFIIH fractions; human transcription reconstitution and hamster repair-deficient extract complementation. The linked 1996 correction page was identified, but its image body could not be retrieved; no assertion that the correction was read. Figures 3–5 are distinct from the correction page’s indexed Figure 2.
Human cyclin-dependent kinase-activating kinase exists in three distinct complexes.
Access: operative original. Original pp. 6489–6490, Methods/Results and Figures 1–2 captions.
Native human HeLa complexes and reciprocal MAT1/XPB immunoprecipitation; CAK–XPD fraction without XPB distinguished. No pure XPB kinase assay.
Access: operative original. Methods p. 15899; Results pp. 15900–15902; Discussion pp. 15902–15903; Figures 1–5 captions; Table I.
Patient XPB TFIIH versus heterozygous maternal control; recombinant human GST-XPB in E. coli. Figure 4 separately measures ATPase/unwinding. No separate linking-number or TC-NER assay.
Access: operative original. Results functional-domain predictions and Role of ERCC3 in XP; Figure 4; Experimental Procedures cell transfection, UV survival, microinjection and repair synthesis.
Human cDNA complements XPB patient-cell repair synthesis, separately from rodent 27-1. DNA-binding/helicase motifs are predictions awaiting assays; no damaged-versus-undamaged binding comparison.
Access: operative original. Author-uploaded original Methods protein production/pull-down; Results Figures 1–3 and recruitment experiments; captions.
Human HeLa XPC–HR23B and recombinant XPC/Sf9, HR23B/E. coli, GST-human TFIIH subunits. Free XPC binds GST-XPB; free HR23B does not. Complex association must not be called a binary RAD23B–XPB assay.
Distinct regions of MAT1 regulate cdk7 kinase and TFIIH transcription activities.
Access: abstract only. PubMed identity/abstract and failed publisher routes.
Original MAT1-domain assays unverified; same-partner human association is independently supported by 8692842.
Dynamic interaction of TTDA with TFIIH is stabilized by nucleotide excision repair in living cells.
Access: operative original. Indexed original blocks 9–14 and 47–56; Results Figure 1C/D and Figure 2C; Methods.
Human fibroblast tagged TTDA/XPD/XPB; co-immunoprecipitation and localization with parental controls. No pure binary interaction inference.
Detection and identification of transcription factors as interaction partners of alien in vivo.
Access: operative original. Author-uploaded four-page original: Methods paragraph p. 993; Results p. 995; Figure 1B caption.
Human U2OS endogenous Alien/COPS2 complex capture, MS identification and co-IP. Complex association, not purified binary contact or XPB corepressor activity.
Access: operative original. Actual author original Results pp. 245–249; Methods p. 254; Figures 1–6 captions.
Human FLAG-XPB proteins in Sf9; human patient TFIIH; human constructs also rescue hamster cells. p52 stimulates XPB ATPase. Directional unwinding in Figure 5B is separable from retained ATPase/repair in T469A/Q638A. No supplement or figure pixels inspected.
Structural basis for group A trichothiodystrophy.
Access: abstract only. PubMed identity/abstract; full original unavailable.
Do not infer misattribution from a yeast-focused title. Human TTDA–XPB association independently established by 16669699.
Access: operative original. Indexed blocks 30–38 and 68–78; Figure 4B versus 4D and Figure 5C; recombinant-complex Methods.
Human TFIIH in Sf9. XPB/XPD complex association differs from direct XPD–p44 binding; Figure 5C is XPD ATPase, not XPB-specific chemistry.
Toward an understanding of the protein interaction network of the human liver.
Access: operative original and target data. Original indexed blocks 11–16, 27–28, 36–37; Supplementary Table S2 row 669; 2017 correction body.
Human liver ORF/library Y2H. Entrez 2071–3839 is ERCC3–KPNA3. Selected follow-up is not universal pair validation. Correction PMID:29254952 corrects an author name, not this dataset.
A proteome-scale map of the human interactome network.
Access: operative original and target data. Actual main original blocks 20–21; official HI-II-14 PSI-MI target rows.
Human Y2H; retested screen pairs XIAP and CEP70 independently located. Orthogonal validation only for subsets; no supplementary Methods or figure pixels read.
A human interactome in three quantitative dimensions organized by stoichiometries and abundances.
Access: abstract only. PubMed identity/abstract; complete operative original unavailable.
Independent same-partner association from 16669699; no original assay, interface or species-specific detail asserted.
Near-atomic resolution visualization of human transcription promoter opening.
Access: operative original. Indexed blocks 7, 22–23, 34–42, 50–51; Results/Figures 3 and 5 and Methods.
HeLa TFIIH/Pol II plus recombinant factors; TBP substitutes for TFIID. Preformed mismatch bubbles/crosslinking; inferred movement between static states is not timed stepping.
Architecture of the human interactome defines protein communities and disease networks.
Access: operative original target data unread. Official BioC original passages 12–19.
Human ORFeome tagged-bait AP-MS, biological versus technical replication and background scoring. Exact TTDA target record not located; independent 16669699 supports the same partner.
Access: operative original and target data. Original blocks 13–20, 47–48, 52–56, 61–62, 67–68; Supplementary Data 2 row 1222, Data 4 row 321, Data 6 row 37.
WT/variant interaction profiles, TRIM27 N355S and XIAP G188E with ERCC3. Disruption=0/intact is not a gain claim. Human proteins assayed in Y2H/PCA; no automatic native-complex extrapolation.
A reference map of the human binary protein interactome.
Access: operative original and target data. Original blocks 7–10 and 53; official HuRI PSI-MI ERCC3 records, with exact line/clone/isoform fields.
Human proteins in yeast two-hybrid. Nine imported pairs match; ADAMTSL4 source partner -3 versus actual dataset -1 is unresolved. Main retest/sequence checks read, no pair-specific mammalian validation assumed.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Access: operative original target data unread. Official BioC passages 99–100, 102, 108–109, 126–127.
Human tagged-bait AP-MS in 293T/HCT116, separately analyzed. Pair-specific TTDA record not inspected; independent 16669699 association used transparently.
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.
Access: operative original target data unread. Official BioC passages 7–13 and 33–34.
Tagged-bait AP-MS in SCC25/CAL33/HET1A with replicate/scoring controls; target XPC–XPB pair not located. Independent actual 10734143 supports the pair, not the specific cancer-screen context.
p53 modulation of TFIIH-associated nucleotide excision repair activity.
Access: abstract only. PubMed identity and abstract; original publisher access insufficient.
p53–XPB direct binding unverified. 8675009 functional p53-rescue experiment is not a new binding assay; holo-TFIIH membership independently established.
Access: operative original. Actual original mirrored PDF through indexed web reader: Results pp. 518–519, Figures 4–6 captions, Methods pp. 522–523, Discussion p. 521.
Human MBP-ERCC3 binding individually translated TFIIE56/34 with controls. HeLa TFIIH recovery on TFIIE resin is a separate experiment. Direct local download returned HTML, not a PDF; evidence is the captured original web text.
Access: abstract only. PubMed identity/abstract and failed publisher routes.
Independent TFIIH subunit associations retained explicitly; exact XPB–XPG context unresolved. No target attribution judgment from abstract/title.
Access: operative original. Original Methods pp. 2275–2276; Results pp. 2278–2280; Figures 2–6 captions; relevant Discussion.
Human XPB bait aa31–742 with mouse embryonic Sug1 library; tagged coexpression validates association. Figures 5–6 recover endogenous human SUG1/XPB. Official P62195 human and P62196 mouse PSMC5 identities checked; not SUG2.
Access: abstract only. PubMed identity/abstract; complete original not recovered.
Independent human TFIIH purification and initiation reconstitution resolve established membership/phase without implying original-specific verification.
Access: abstract only. PubMed identity/abstract and publisher preview, not complete original.
Human TFIIH membership independently established. Linked CommentIn records are commentary, not retraction or correction.
Access: abstract only. PubMed identity/positive abstract; EPMC/PMC/BioC retrieval failures.
Patient repair-factor recruitment/retention abstract supports relevance; exact localization causality unresolved. Independent human repair assays resolve NER and UV-response biology.
TFIIH: when transcription met DNA repair.
Access: review preview only. PubMed identity/abstract and publisher key points/figure summaries; full review not recovered. Actual publisher erratum read.
Secondary review. Erratum corrects XPD helicase direction in Table 1, not an XPB motor assay. Original independent assays support review-linked repair/initiation claims.
The XPB and XPD DNA helicases are components of the p53-mediated apoptosis pathway.
Access: operative original. Actual author original OCR pp. 1221–1223 and 1226–1227; Figure 4B and Tables 2–3; Results/Discussion.
Human XPB patient fibroblasts, p53 overexpression and WT XPB coinjection rescue; delayed rather than universally absent apoptosis. Adriamycin/Fas lymphoblast experiments concern XPD, not XPB. No figure pixels or complete supplementary/Methods reading claimed.
Genetic susceptibility of newborn daughters to oxidative stress.
Access: abstract only. PubMed identity/abstract; complete original unavailable.
Human peroxide-response context does not resolve exact XPB perturbation/control scope. No wrong-gene conclusion from foregrounded genotypes.
Trichothiodystrophy, a transcription syndrome.
Access: review abstract only. PubMed identity and abstract; publisher access blocked.
Hair-cell differentiation term has epidermal and neuronal branches. No universal inner-ear interpretation; experimental lineage/species/XPB role unresolved.
Access: abstract only. PubMed identity and positive abstract; operative original unavailable.
HepG2 XPB overexpression/apoptosis context not independently verified. Same broad positive-regulatory claim independently supported in a different human fibroblast context by 8675009.
DNA nucleotide excision repair-dependent signaling to checkpoint activation.
Access: operative original. Original indexed blocks 24–27 and 34–44, UV signaling Results and Methods.
Human primary fibroblasts including two XPB mutants; UV Chk1/p53 phosphorylation differs by proliferation state. No XPB kinase or direct full transition-kinetics assay.
Publisher/DOI; actual original access.
All five scanned pages 10718–10722, including Methods 10718–10719, Results 10719–10720, Figures 1–3 and Table 1. Figure pixels actually inspected. Yeast Rad25/Ssl2 copurifies with Rad2 and core TFIIH; the preparation supports reconstituted incision.
Yeast complex; not an isolated human XPB endonuclease assay or a human isoform assignment.
Publisher/DOI; actual original access.
Results indexed blocks 54–62,65–69,71,74–75; Discussion 84–85; Methods 90,93,95,97,102. Yeast Ssl2 crosslinking in immobilized promoter PICs, with the Figure 6–8 captions.
Main operative text and captions only; no supplementary files or image pixels. Translocase description here is a proposed mechanistic model, not a direct human motor assay.
Publisher/DOI; actual original access.
Results blocks 31,34–35,37,39; main Methods 71; Figure 2 caption and actual Figure 2 pixels. Mouse postnatal liver XPB ChIP at Igf1, GhR, Dio1 and PrlR promoters, with nonpromoter/inactive-gene controls.
Main Methods delegates details to SI and prior work. The attempted SI retrieval returned HTML, not a PDF. This is promoter-associated chromatin occupancy, not purified sequence-specific DNA recognition.
Publisher/DOI; actual original access.
Publisher-permitted article reprint in thesis: permission p58; Methods pp 62–68 and Results pp 69–76/Figs 2.2–2.6 captions (text lines3440–4180). Rat GD10–12 embryo/yolk-sac NER expression profiling; XPB transcript and protein measurements; teratogen exposure.
Text/captions read, no independent figure-pixel inspection for this source. Expression during organogenesis and a nonspecific teratogen do not establish an XPB-executed organ-development step.
Publisher/DOI; actual original access.
Author-uploaded original: Results pp 2882–2885/web384–640 and Figure 3 caption/web764–782; Methods pp 2890–2891/web1503–1751. Human HeLa triptolide versus alpha-amanitin, RNA readouts and XPB ChIP are separated from mouse ES mutant experiments.
No figure pixels or supplement. This is inhibitor/occupancy evidence, not purified XPB ATPase measurement. An initial guessed Oxford URL used wrong pagination and failed403; it is not evidence of original unavailability. Verified citation is HMG22(14):2881–2893.
Publisher/DOI; actual original access.
Results pp 248–249/web533–698, Figure 3–5 captions/web906–990; Methods p254/web1096–1265. Recombinant human XPB expressed in Sf9, immunopurified bidirectional M13 unwinding, ATPase and TFIIH NER assays. Figure 5B reports 3′–5′ helicase activity; helicase-impaired T469A/Q638A retain ATPase and repair, whereas K346R does not.
No figure pixels inspected for this source. CHO host-cell complementation uses human XPB transgene, distinct from purified recombinant and native human-cell TFIIH assays.
Publisher/DOI; actual original access.
Independently read Results 46–51, Figure 5 caption48, Methods 56,60–61,68–69: recombinant human Core7 with separate XPB K346R and XPD K48R mutants, ATPase and bubble formation/enlargement.
Figure 5 was inspected separately; the main-text and caption assessment is corroborated by that image inspection. The two-stroke translocation diagram is a model; ATP/ADP was not visualized in the relevant No-G/DuIS structures. Does not erase the historical isolated XPB unwinding assay.
Publisher/DOI; actual original access.
Independently read original indexed blocks 7,22–23,34–42,50–51: HeLa-derived TFIIH and Pol II, recombinant general factors and TBP substituted for TFIID, premelted mismatch scaffolds; XPB duplex-DNA engagement in static PIC states.
No image or supplemental inspection for this source. The 12-bp displacement is inferred between structural states, not real-time stepping. PIC preparation does not establish TFIID membership.
The PANTHER tree and MSA, service version19, contain human P19447 at PTN002477849. Its ungapped aligned sequence exactly matches the official 782-residue canonical sequence. The current IBD file places the assigned assertions at PTN000138598 (Eukaryota), PTN000138606 (Theria) and PTN000138607 (Eutheria). All lie on the target path; no NOT record intervenes in this saved current-IBD path. This verifies topology and alignment identity, not a new all-family functional reconstruction. Human self-WITH entries are legitimate descendant experimental evidence.
The rat Ercc3 donor Q4G005/RGD1307139 for embryonic organ development is IEP/PMID:11425516. Its actual expression study does not establish an XPB-specific developmental step; the proposed MAO concerns evidence scope, not correct node ancestry. For hair-cell differentiation, the correct Theria node inherits human evidence from PMID:11335038, a review available only as a verified abstract. Its positive hair-dysplasia discussion does not settle differentiation versus hair-shaft/mature-cell effects. GO:0035315 is not restricted to inner-ear sensory cells.
Mouse P49135 carries the promoter-chromatin IDA PMID:22323595; actual Figure 2 and promoter/nonpromoter controls support transfer. Its ATPase IMP citation23562818 is distinguished from the independently read human biochemical assays. No ARBA assertion occurs for this source.
InterPro target matches identify IPR001161 at 60–779 and IPR006935 at 315–471, with the imported GO mappings. This resolves an apparent difference between the UniProt cross-reference subset and the full InterPro target-match response; neither family identity nor label was guessed. Rhea13065 supplies ATP-hydrolysis chemistry, kept separately from motor movement.
HPA ERCC3 actual XML reports supported ICC/IF nucleoplasm localization in A-431, U-251MG and U2OS with CAB037153 and HPA046077. These target antibody records support nucleus→nucleoplasm refinement. They do not identify a natural alternative product; none was supplied by the frozen UniProt source. No independent HPA image scoring was performed.
Every one of the 73 Reactome source rows has a forward participant path to ERCC3 entity 67439: human P19447, residues1–782, compartment nucleoplasm. The 66 location rows are not converted into catalytic assertions for whichever enzyme executes the event. The four helicase rows use catalyst 109879 or catalyst 9684122, whose activeUnit specifically names ERCC3. These are not XPD-subunit transfers. The source-specific paths and events follow.
| Seed index | Original source | Participant route to ERCC3 |
|---|---|---|
| 51 | R-HSA-109639: Formation of the closed pre-initiation complex | 109639 —input→109634 —hasComponent→67439 |
| 52 | R-HSA-111264: Addition of nucleotides between position +11 and +30 | 111264 —input→75902 —hasComponent→109634 —hasComponent→67439 |
| 53 | R-HSA-112379: Recruitment of elongation factors to form elongation complex | 112379 —input→109634 —hasComponent→67439 |
| 54 | R-HSA-112383: Hypophosphorylation of RNA Pol II CTD by FCP1P protein | 112383 —input→109634 —hasComponent→67439 |
| 55 | R-HSA-112385: Addition of nucleotides leads to transcript elongation | 112385 —output→109634 —hasComponent→67439 |
| 56 | R-HSA-113430: Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex | 113430 —input→111261 —hasComponent→109634 —hasComponent→67439 |
| 57 | R-HSA-5689317: Formation of the pre-incision complex in GG-NER | 5689317 —input→6790517 —hasComponent→5689624 —hasComponent→67439 |
| 58 | R-HSA-5689861: Recruitment of XPA and release of CAK | 5689861 —input→5689862 —hasComponent→109634 —hasComponent→67439 |
| 59 | R-HSA-5690213: DNA polymerases delta, epsilon or kappa bind the GG-NER site | 5690213 —input→5691059 —hasComponent→5689624 —hasComponent→67439 |
| 60 | R-HSA-5690988: 3'-incision of DNA by ERCC5 (XPG) in GG-NER | 5690988 —output→5689624 —hasComponent→67439 |
| 61 | R-HSA-5690990: 5'- incision of DNA by ERCC1:ERCC4 in GG-NER | 5690990 —output→5691059 —hasComponent→5689624 —hasComponent→67439 |
| 62 | R-HSA-5690991: Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in GG-NER | 5690991 —input→5691043 —hasComponent→6790517 —hasComponent→5689624 —hasComponent→67439 |
| 63 | R-HSA-5690996: ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA | 5690996 —output→5691018 —hasComponent→5689624 —hasComponent→67439 |
| 64 | R-HSA-5691000: TFIIH binds GG-NER site to form a verification complex | 5691000 —input→109634 —hasComponent→67439 |
| 65 | R-HSA-5696670: CHD1L is recruited to GG-NER site | 5696670 —input→5689300 —hasComponent→5689624 —hasComponent→67439 |
| 66 | R-HSA-6781818: RNA Pol II initiates transcription from damaged DNA template | 6781818 —input→109634 —hasComponent→67439 |
| 67 | R-HSA-6781824: Active RNA Pol II complex transcribes lesion-containing DNA template | 6781824 —input→6781821 —hasComponent→109634 —hasComponent→67439 |
| 68 | R-HSA-6781833: ERCC8 (CSA) binds stalled RNA Pol II | 6781833 —input→6781837 —hasComponent→6781822 —hasComponent→109634 —hasComponent→67439 |
| 69 | R-HSA-6781840: ERCC6 binds stalled RNA Pol II | 6781840 —input→6781822 —hasComponent→109634 —hasComponent→67439 |
| 70 | R-HSA-6781867: ERCC8:DDB1:CUL4:RBX1 ubiquitinates ERCC6 and RNA Pol II | 6781867 —input→6781839 —hasComponent→6781837 —hasComponent→6781822 —hasComponent→109634 —hasComponent→67439 |
| 71 | R-HSA-6782004: Assembly of the pre-incision complex in TC-NER | 6782004 —input→6781866 —hasComponent→6781848 —hasComponent→6781861 —hasComponent→109634 —hasComponent→67439 |
| 72 | R-HSA-6782069: UVSSA:USP7 deubiquitinates ERCC6 | 6782069 —input→6782063 —hasComponent→6781866 —hasComponent→6781848 —hasComponent→6781861 —hasComponent→109634 —hasComponent→67439 |
| 73 | R-HSA-6782131: ERCC2-facilitated RNA Pol II backtracking in TC-NER | 6782131 —output→9684117 —hasComponent→9684121 —hasComponent→9684120 —hasComponent→9684119 —hasComponent→109634 —hasComponent→67439 |
| 74 | R-HSA-6782138: ERCC5 and RPA bind TC-NER site | 6782138 —input→6782111 —hasComponent→6782122 —hasComponent→6782112 —hasComponent→6782116 —hasComponent→109634 —hasComponent→67439 |
| 75 | R-HSA-6782141: Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in TC-NER | 6782141 —input→6782134 —hasComponent→6782111 —hasComponent→6782122 —hasComponent→6782112 —hasComponent→6782116 —hasComponent→109634 —hasComponent→67439 |
| 76 | R-HSA-6782204: 5' incision of damaged DNA strand by ERCC1:ERCC4 in TC-NER | 6782204 —output→6782205 —hasComponent→109634 —hasComponent→67439 |
| 77 | R-HSA-6782208: Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER | 6782208 —input→6782222 —hasComponent→109634 —hasComponent→67439 |
| 78 | R-HSA-6782211: DNA polymerases delta, epsilon or kappa bind the TC-NER site | 6782211 —input→6782205 —hasComponent→109634 —hasComponent→67439 |
| 79 | R-HSA-6782224: 3' incision by ERCC5 (XPG) in TC-NER | 6782224 —input→6782219 —hasComponent→109634 —hasComponent→67439 |
| 80 | R-HSA-6782227: Ligation of newly synthesized repair patch to incised DNA in TC-NER | 6782227 —input→6782220 —hasComponent→109634 —hasComponent→67439 |
| 81 | R-HSA-6782234: Recovery of RNA synthesis after TC-NER | 6782234 —output→109634 —hasComponent→67439 |
| 82 | R-HSA-6790454: SUMOylation of XPC | 6790454 —input→5691018 —hasComponent→5689624 —hasComponent→67439 |
| 83 | R-HSA-6790487: RNF111 ubiquitinates SUMOylated XPC | 6790487 —input→6790468 —hasComponent→5689624 —hasComponent→67439 |
| 84 | R-HSA-6797606: CDK12 phosphorylates RNA Pol II CTD at DNA repair genes | 6797606 —input→6797614 —hasComponent→6797611 —hasComponent→109634 —hasComponent→67439 |
| 85 | R-HSA-6797616: CCNK:CDK12 binds RNA Pol II at DNA repair genes | 6797616 —input→6797611 —hasComponent→109634 —hasComponent→67439 |
| 86 | R-HSA-73758: Recruitment of RNA Polymerase I:RRN3 to the 45S pre-rRNA gene | 73758 —input→109634 —hasComponent→67439 |
| 87 | R-HSA-73769: Loss of RRN3 from RNA Polymerase I promoter escape complex | 73769 —input→73716 —hasComponent→109634 —hasComponent→67439 |
| 88 | R-HSA-73946: Abortive initiation after formation of the first phosphodiester bond | 73946 —output→109634 —hasComponent→67439 |
| 89 | R-HSA-74986: Elongation of pre-rRNA transcript | 74986 —input→73717 —hasComponent→109634 —hasComponent→67439 |
| 90 | R-HSA-74992: Dissociation of PTRF:RNA Polymerase I:pre-rRNA complex | 74992 —output→109634 —hasComponent→67439 |
| 91 | R-HSA-74993: PTRF binds the paused RNA Polymerase I complex | 74993 —input→74979 —hasComponent→73717 —hasComponent→109634 —hasComponent→67439 |
| 92 | R-HSA-74994: Elongating RNA Polymerase I Transcription Complex pauses at the TTF1:Sal Box | 74994 —input→9988366 —hasComponent→73717 —hasComponent→109634 —hasComponent→67439 |
| 93 | R-HSA-75850: Addition of the third nucleotide on the nascent transcript | 75850 —input→109878 —hasComponent→109634 —hasComponent→67439 |
| 94 | R-HSA-75856: Abortive Initiation Before Second Transition | 75856 —output→109634 —hasComponent→67439 |
| 95 | R-HSA-75861: NTP Binds Active Site of RNA Polymerase II | 75861 —input→109876 —hasComponent→109634 —hasComponent→67439 |
| 96 | R-HSA-75862: Fall Back to Closed Pre-initiation Complex | 75862 —input→109876 —hasComponent→109634 —hasComponent→67439 |
| 97 | R-HSA-75864: Newly Formed Phosphodiester Bond Stabilized and PPi Released | 75864 —input→83601 —hasComponent→109634 —hasComponent→67439 |
| 98 | R-HSA-75866: Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP | 75866 —output→83601 —hasComponent→109634 —hasComponent→67439 |
| 99 | R-HSA-75869: Addition of the fourth nucleotide on the Nascent Transcript: Second Transition | 75869 —input→75878 —hasComponent→109634 —hasComponent→67439 |
| 100 | R-HSA-75873: Addition of Nucleotides 5 through 9 on the growing Transcript | 75873 —input→75881 —hasComponent→109634 —hasComponent→67439 |
| 101 | R-HSA-75891: Abortive Initiation After Second Transition | 75891 —output→109634 —hasComponent→67439 |
| 102 | R-HSA-75949: RNA Polymerase II Promoter Opening: First Transition | 75949 —catalystActivity→109879 —activeUnit→67439 |
| 103 | R-HSA-76576: Addition of nucleotides 10 and 11 on the growing transcript: Third Transition | 76576 —input→75882 —hasComponent→109634 —hasComponent→67439 |
| 104 | R-HSA-77068: Activation of GT | 77068 —input→77053 —hasComponent→109634 —hasComponent→67439 |
| 105 | R-HSA-77069: RNA Polymerase II CTD (phosphorylated) binds to CE | 77069 —input→157174 —hasComponent→109634 —hasComponent→67439 |
| 106 | R-HSA-77071: Phosphorylation (Ser5) of RNA pol II CTD | 77071 —input→157171 —hasComponent→109634 —hasComponent→67439 |
| 107 | R-HSA-77073: SPT5 subunit of Pol II binds the RNA triphosphatase (RTP) | 77073 —input→77056 —hasComponent→109634 —hasComponent→67439 |
| 108 | R-HSA-77077: Capping complex formation | 77077 —input→77061 —hasComponent→109634 —hasComponent→67439 |
| 109 | R-HSA-77078: Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme | 77078 —input→77063 —hasComponent→77061 —hasComponent→109634 —hasComponent→67439 |
| 110 | R-HSA-77081: Formation of the CE:GMP intermediate complex | 77081 —input→77064 —hasComponent→77061 —hasComponent→109634 —hasComponent→67439 |
| 111 | R-HSA-77083: Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA | 77083 —output→77066 —hasComponent→77061 —hasComponent→109634 —hasComponent→67439 |
| 112 | R-HSA-77085: Dissociation of transcript with 5'-GMP from GT | 77085 —input→77066 —hasComponent→77061 —hasComponent→109634 —hasComponent→67439 |
| 113 | R-HSA-77090: Methylation of GMP-cap by RNA Methyltransferase | 77090 —output→109634 —hasComponent→67439 |
| 114 | R-HSA-9613494: Unwinding of DNA for the Nascent Transcript: Second Transition | 9613494 —catalystActivity→109879 —activeUnit→67439 |
| 115 | R-HSA-9613497: Unwinding DNA for the nascent transcript | 9613497 —catalystActivity→109879 —activeUnit→67439 |
| 116 | R-HSA-9684118: ERCC3-facilitated RNA Pol II backtracking in TC-NER | 9684118 —catalystActivity→9684122 —activeUnit→67439 |
| 125 | R-HSA-6781827: Transcription-Coupled Nucleotide Excision Repair (TC-NER) | 6781827 —hasEvent→6782234 —output→109634 —hasComponent→67439 |
| 133 | R-HSA-73857: RNA Polymerase II Transcription | 73857 —hasEvent→674695 —hasEvent→73946 —output→109634 —hasComponent→67439 |
| 138 | R-HSA-73776: RNA Polymerase II Promoter Escape | 73776 —hasEvent→9613497 —catalystActivity→109879 —activeUnit→67439 |
| 154 | R-HSA-75949: RNA Polymerase II Promoter Opening: First Transition | 75949 —catalystActivity→109879 —activeUnit→67439 |
| 155 | R-HSA-9613494: Unwinding of DNA for the Nascent Transcript: Second Transition | 9613494 —catalystActivity→109879 —activeUnit→67439 |
| 156 | R-HSA-9613497: Unwinding DNA for the nascent transcript | 9613497 —catalystActivity→109879 —activeUnit→67439 |
| 157 | R-HSA-9684118: ERCC3-facilitated RNA Pol II backtracking in TC-NER | 9684118 —catalystActivity→9684122 —activeUnit→67439 |
GO:0043138 currently has a 3′–5′ helicase label but a definition describing the opposite direction; OLS independently reproduces the inconsistency. The actual EC5.6.2.4 record describes 3′–5′ movement. Imported IDs/labels remain intact; assay direction comes from the actual human original.
GO:0015616 describes ATP-driven DNA movement and is currently unrestricted MF. It is used for the principal motor refinement, while GO:0016887 retains separately measured ATP chemistry. Neither is inferred to be the other’s current ontology ancestor.
Reactome 73776 models promoter escape. Current GO:0006367 and its initiation parent explicitly distinguish clearance from initiation, while GO:0006368 starts after clearance. GO:0001111 therefore supplies the source-specific promoter-clearance replacement; its ancestry includes transcription by Pol II, not initiation or elongation.
The backtracking discussion in Reactome 9684118 uses a bacterial UvrD analogy. Retaining an independently measured human helicase capacity does not certify every modeled human backtracking step. The 9613494/9613497 event objects also use nucleotide-product representations that should not replace actual XPB phosphate-release chemistry; no claim of AMP/PPi production by XPB is made.
Original article. Main Methods, Results and Discussion were inspected, including the acute-depletion PRO-seq experiments and controls. Endogenous FKBP-tagged human HAP1 factors were depleted for two hours; moth-nuclei spike-ins and untagged drug controls support the transcription comparison. XPB dependence is variable across promoters, and residual protein remains. No figure pixels or supplementary files were inspected. The 2026 Communications Biology item DOI 10.1038/s42003-026-10203-1 is a Perspective, not an additional primary experimental study.
Fresh official ATP hydrolysis and DNA translocase definitions and typed ancestry distinguish chemical ATP turnover from the overall ATP-driven motor action. Both are represented as activities of the same XPB molecule. The hydrolysis entry uses the already inspected human primary experiments described above and adds no new process assertion or quotation.
Official O00505 identifies human KPNA3 as an importin-alpha family member. GO:0061676 requires binding to that family; the exact liver-screen and HuRI records documented above support this refinement. They do not establish physiological cargo transport or receptor activity by XPB. The current GO:0043138 label/definition polarity mismatch remains documented; no imported identifier or label was altered.