This guide links each directly cited paper to the experimental evidence used in the annotation review. Access to a main article is distinguished from access to a target-specific supplementary record, and figure captions from inspected image data. Publication-cache availability flags are preserved independently of these assessments.
The experimentally characterized full-length human protein and canonical database entities refer to the 760-residue XPD product. The 405-residue splice product is not assumed to share these functions. Human proteins expressed in insect or bacterial hosts remain human preparations; yeast donor experiments are identified separately.
Original access route; identifier record.
Actual original scans pp6483–6486, Figures 2–5, Methods and captions read; p6484/Figure 2 pixels inspected. Human HeLa CAK/XPD and TFIIH preparations, transcription reconstitution, and human fractions complementing hamster-cell NER extracts. Historical TFIIH* lacks XPD and is distinct from the current seven-subunit core definition.
Original access route; identifier record.
Actual original scans pp6489–6492, Methods and Figures 3–6 read; p6492/Figure 6 pixels inspected. Native human HeLa TFIIH/CAK–ERCC2 isolation and transcription reconstitution. The kinase belongs to CAK, not XPD; a murine promoter DNA template does not change the human protein origin.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified. Complete JBC original not recovered. Its MAT1–XPD assay was not inspected; the protein-complex scaffold role is independently established by actual human CAK–ERCC2 reconstitution and TFIIH architecture in PMID:8692842 and PMID:31253769, rather than assumed verification of this source.
Original access route; identifier record.
Official identifier/title/DOI verified. Indexed original p35329 Methods/initial Results fragments cover human HeLa-library constructs, Sf9 coexpression and assay protocols, but complete main Results and figures were not recovered. Same-partner XPD/p44 and CAK–core scaffold biology is independently supported by PMID:19934020 and PMID:8692842; that does not verify this original assay in full.
Original access route; identifier record.
Actual full original operative Methods, Results and Figures 1–2 captions read. Full-length human XPD-GFP in XP-D fibroblasts complements UV sensitivity, coimmunoprecipitates XPB, and displays nuclear/cytoplasmic pools. No image pixels or supplementary material inspected.
Original access route; identifier record.
Actual original Results/Figures 3–6 captions and operative Methods read. Human XPD variant/TFIIH preparations, direct p44 coexpression/co-IP, ATPase, helicase, NER and transcription assays distinguish catalytic defects from complex architecture. No figure pixels/supplement read; engineered disease truncations are not the natural 405-aa product.
Original access route; identifier record.
Official identifier/title/DOI and positive abstract verified. Full operative original was not recovered from bounded publisher/alternate routes. The abstract reports MMXD, spindle localization and segregation phenotypes; no original microscopy, purification controls or knockdown/rescue details were inspected. Independent CIA-client binding papers resolve some partners, not the complete named complex or mitotic phenotype.
Original access route; identifier record.
Actual original Experimental Procedures, Results and Figures 2–4 captions read. Human-cell fractionation/co-purification and Figure 4E recombinant human-XPD pairwise binding support CIA client interactions. No figure pixels/supplement read; a client relationship is not XPD Fe–S assembly catalysis.
Original access route; identifier record.
Actual main CIA-interaction Results, Figure 5D/6 captions and human-cell affinity/MudPIT Methods read. Exact TableS4 target records remain unread; independently inspected PMID:23585563 and PMID:28178521 establish the same XPD partners. Separate mouse CIA2A constructs are not relabeled as human XPD assays.
Original access route; identifier record.
Actual main human ORF Y2H design, retest/identity-confirmation Methods and data availability read. The ERCC2–GTF2H2C record in TableS2G was not recovered, so target-pair support remains unresolved. Orthogonal validation of a subset cannot be assigned to this pair without its record. Main article access is distinguished from missing supplementary pair evidence.
Original access route; identifier record.
Actual human PIC/TFIIH Results and Methods, Figure 3f and Extended Data6 captions read. TFIIH and PolII were purified from HeLa nuclei; TBP was used in place of TFIID. The complex source supports TFIIH membership, not TFIID. Local resolution and homology modelling bound pairwise-contact interpretation; no figure pixels inspected.
Original access route; identifier record.
Actual main XPD-binding Results/Figures 4/6 and operative Methods read, plus supplemental PDF p3/Figure S2A/B text and pixels. WT/C190S XPD recover MMS19, CIAO1 and MIP18 in co-IP; endogenous human XPD supports MMS19 association. This is client binding, not XPD Fe–S transfer catalysis; no natural-product equivalence is inferred.
Original access route; identifier record.
Actual main qHT-dS BRET Results and Methods read: human WT/mutant ORFs, expression normalization, titration and replicate controls in HEK293T. The exact ERCC2–BRAF supplementary record and allele context were not recovered. Main original access does not establish target-pair support or whether it is WT versus mutation-specific.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified; publisher provides preview, not the operative original binding experiment. PMID:8675009 supports a contextual p53-dependent apoptosis phenotype but cites earlier interaction work rather than repeating the XPD–p53 binding assay in the inspected blocks.
Original access route; identifier record.
Official identifier/title/DOI and positive human-TFIIH interaction abstract verified; complete ACS original not recovered. The precise imported pair assays were not inspected. Independent human co-IP, p44 interface/function and XPG crosslink studies are explicitly identified in the relevant reviews; they do not imply this original was read.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified; complete original not recovered. The abstract distinguishes engineered XPD mutants in live-cell repair/damage association from biochemical assays on an archaeal homolog. The archaeal enzymology is not presented as human enzymology, and independent human localization resolves the imported nucleus row.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified; complete original not recovered. Abstract describes functional human HeLa FLAG-p62 TFIIH. Independently inspected human TFIIH purification/reconstitution supports the same complex/initiation biology without claiming this source Methods were inspected.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified; publisher preview did not expose operative full text. Independent human TFIIH originals support the imported holo-complex location; no uninspected source-specific assay detail is inferred.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified; complete JBC original not recovered. XPB-focused patient TFIIH results in the abstract do not prove XPD was untested. Independent human XPD helicase/initiation evidence resolves those functions, while the source-specific transcription-coupled repair assertion remains uncertain.
Original access route; identifier record.
Actual original scans pp1438–1439 Results/Figure 3 caption and pp1445–1446 Methods/conclusions read through OCR. Human genomic/cDNA sequences were tested in hamster UV5; partial-cDNA transient rescue differs from genomic complementation. Helicase chemistry is inferred from sequence here and directly measured in later sources. No scan pixels inspected.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified; complete review not recovered from the publisher preview. Independent original human reconstitution and repair assays establish the cited repair/initiation functions. No source-specific full-text or linked change-history content is claimed as read.
Original access route; identifier record.
Actual author-hosted original PDF: Results pp1221/1223–1224, Table 3/Figure 4B, plasmid paragraph p1228 and Methods p1229 read; Figure 4/Table 3 page pixels inspected. Human XP-D fibroblast p53-induced apoptosis and wild-type XPD rescue are positive, with retained p21 induction. This is not a new direct XPD–p53 binary binding assay.
Original access route; identifier record.
Official identifier/title/DOI and abstract verified; complete original not recovered. Human mother–newborn genotype/oxidative-damage setting alone does not settle the XPD-specific result or imported IMP mechanism; retain uncertainty rather than infer absence or misattribution.
Original access route; identifier record.
Official identifier/title/DOI and positive human XPD ATPase/helicase abstract verified; complete Nature original unavailable beyond preview. Independent human ATPase and directional/K48R unwinding experiments in PMID:19934020 and PMID:31253769 establish those activities without pretending this original assay was inspected.
Original access route; identifier record.
Official identifier/title/DOI and positive XPD/p44 interface abstract verified; complete Nature original unavailable beyond preview. Later actual human XPD/p44 interaction, ATPase and helicase assays independently support the refined catalytic function.
Original access route; identifier record.
Official identifier/title/DOI and TTD/hair-dysplasia abstract verified; complete review and its primary differentiation evidence were not recovered. Current GO:0035315 has both epidermal-cell and neuron-differentiation direct parents, so no universal inner-ear interpretation or source error is inferred. Exact cell type and evidence remain unresolved.
Original access route; identifier record.
Actual original main Results, operative Methods and captions read, with Figure 1 pixels and supplemental PDF p2/Figure S1 text/pixels. Insect-expressed human full-length XPD in seven-subunit TFIIH drives 5′–3′ unwinding lost with K48R; XPB triplex displacement is separate. Tags removed. Lesion-free structural DNA does not itself prove damaged-DNA selectivity; other supplements/raw crosslinks/movies unread. Supplemental CDK7 assay uses yeast PolII substrate.
Original access route; identifier record.
Actual original Results, Discussion, Methods and captions read. Primary human XPD-mutant fibroblasts show context-dependent UV-induced Chk1/p53 phosphorylation (Figures 4–5), with XP-D/CS exceptions. The measured endpoint is checkpoint signaling, not direct phase-transition kinetics or XPD kinase activity. No figure pixels/supplement inspected.
The official PTHR11472 tree places human leaf PTN002479324 beneath both actual asserted nodes: PTN000158192 (DNA helicase) and PTN000158239 (damaged-DNA binding, nucleus, nucleotide-excision repair, RNA polymerase II transcription). All five exact IBD records were inspected. The human aligned sequence matches canonical P18074 at all 760 residues; no NOT record occurs on the saved target ancestry. Yeast RAD3 leaf PTN000158285 descends from PTN000158239 and its current GOA damaged-DNA IDA points to PMID:8132553. No donor-count heuristic or self-WITH circularity claim is used. PANTHER tree source.
The imported six InterPro entries are present in the official target UniProt cross-references. Their mappings support DNA/helicase/ATP functions; generic domain descriptions do not establish RNA catalysis. The IPR001945 entry contains an incongruous XPG/ERCC5 introductory passage; its RAD3/XPD identity, target membership and GO mappings are independently verified, so that unrelated endonuclease prose is not transferred to ERCC2. InterPro IPR001945.
Rhea13065 specifies ATP hydrolysis. EC5.6.2.3 specifies ATP-coupled 5′–3′ DNA helicase; generic replication-fork examples do not assign ERCC2 a replication-specific role. Current QuickGO definitions and ancestry were inspected for all authored replacement terms. The helicase refinement describes the informative motor activity; it does not claim GO:0043139 is an is_a child of the broad phosphorus-anhydride hydrolase term.
The actual ERCC2 Human Protein Atlas record and XML report antibody HPA069266, supported nucleoplasmic localization in SiHa, U-251MG and U2OS cells and additional cytosol in U-251MG. Structured assay data and reliability were read, not image pixels; these observations are not isoform-resolved.
All 68 row contexts (67 distinct source objects) reach ERCC2 entity R-HSA-67443, whose own reference is P18074, coordinates 1–760 and compartment nucleoplasm (GO:0005654). Each source's forward participant/component path is recorded below. These support the target location without assigning ERCC2 the polymerase, nuclease, capping, kinase or ubiquitin-transfer work carried out by other members. Event6782131 has catalyst 6782120 with ERCC2 as its explicit active unit; its detailed backtracking description is a mechanistic model, while human DNA-helicase activity is independently demonstrated.
| Annotation index (zero-based) | Source event | Forward path to target |
|---|---|---|
| 43 | R-HSA-109639 Formation of the closed pre-initiation complex | 109639 → 109634 → 67443 |
| 44 | R-HSA-111264 Addition of nucleotides between position +11 and +30 | 111264 → 75902 → 109634 → 67443 |
| 45 | R-HSA-112379 Recruitment of elongation factors to form elongation complex | 112379 → 109634 → 67443 |
| 46 | R-HSA-112383 Hypophosphorylation of RNA Pol II CTD by FCP1P protein | 112383 → 109634 → 67443 |
| 47 | R-HSA-112385 Addition of nucleotides leads to transcript elongation | 112385 → 109634 → 67443 |
| 48 | R-HSA-113430 Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex | 113430 → 111261 → 109634 → 67443 |
| 49 | R-HSA-5689317 Formation of the pre-incision complex in GG-NER | 5689317 → 6790517 → 5689624 → 67443 |
| 50 | R-HSA-5689861 Recruitment of XPA and release of CAK | 5689861 → 5689862 → 109634 → 67443 |
| 51 | R-HSA-5690213 DNA polymerases delta, epsilon or kappa bind the GG-NER site | 5690213 → 5691059 → 5689624 → 67443 |
| 52 | R-HSA-5690988 3'-incision of DNA by ERCC5 (XPG) in GG-NER | 5690988 → 5689624 → 67443 |
| 53 | R-HSA-5690990 5'- incision of DNA by ERCC1:ERCC4 in GG-NER | 5690990 → 5691059 → 5689624 → 67443 |
| 54 | R-HSA-5690991 Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in GG-NER | 5690991 → 5691043 → 6790517 → 5689624 → 67443 |
| 55 | R-HSA-5690996 ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA | 5690996 → 5691018 → 5689624 → 67443 |
| 56 | R-HSA-5691000 TFIIH binds GG-NER site to form a verification complex | 5691000 → 109634 → 67443 |
| 57 | R-HSA-5696670 CHD1L is recruited to GG-NER site | 5696670 → 5689300 → 5689624 → 67443 |
| 58 | R-HSA-6781818 RNA Pol II initiates transcription from damaged DNA template | 6781818 → 109634 → 67443 |
| 59 | R-HSA-6781824 Active RNA Pol II complex transcribes lesion-containing DNA template | 6781824 → 6781821 → 109634 → 67443 |
| 60 | R-HSA-6781833 ERCC8 (CSA) binds stalled RNA Pol II | 6781833 → 6781837 → 6781822 → 109634 → 67443 |
| 61 | R-HSA-6781840 ERCC6 binds stalled RNA Pol II | 6781840 → 6781822 → 109634 → 67443 |
| 62 | R-HSA-6781867 ERCC8:DDB1:CUL4:RBX1 ubiquitinates ERCC6 and RNA Pol II | 6781867 → 6781839 → 6781837 → 6781822 → 109634 → 67443 |
| 63 | R-HSA-6782004 Assembly of the pre-incision complex in TC-NER | 6782004 → 6781866 → 6781848 → 6781861 → 109634 → 67443 |
| 64 | R-HSA-6782069 UVSSA:USP7 deubiquitinates ERCC6 | 6782069 → 6782063 → 6781866 → 6781848 → 6781861 → 109634 → 67443 |
| 65 | R-HSA-6782131 ERCC2-facilitated RNA Pol II backtracking in TC-NER | 6782131 → 6782120 → 67443 |
| 66 | R-HSA-6782138 ERCC5 and RPA bind TC-NER site | 6782138 → 6782111 → 6782122 → 6782112 → 6782116 → 109634 → 67443 |
| 67 | R-HSA-6782141 Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in TC-NER | 6782141 → 6782134 → 6782111 → 6782122 → 6782112 → 6782116 → 109634 → 67443 |
| 68 | R-HSA-6782204 5' incision of damaged DNA strand by ERCC1:ERCC4 in TC-NER | 6782204 → 6782205 → 109634 → 67443 |
| 69 | R-HSA-6782208 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER | 6782208 → 6782222 → 109634 → 67443 |
| 70 | R-HSA-6782211 DNA polymerases delta, epsilon or kappa bind the TC-NER site | 6782211 → 6782205 → 109634 → 67443 |
| 71 | R-HSA-6782224 3' incision by ERCC5 (XPG) in TC-NER | 6782224 → 6782219 → 109634 → 67443 |
| 72 | R-HSA-6782227 Ligation of newly synthesized repair patch to incised DNA in TC-NER | 6782227 → 6782220 → 109634 → 67443 |
| 73 | R-HSA-6782234 Recovery of RNA synthesis after TC-NER | 6782234 → 109634 → 67443 |
| 74 | R-HSA-6790454 SUMOylation of XPC | 6790454 → 5691018 → 5689624 → 67443 |
| 75 | R-HSA-6790487 RNF111 ubiquitinates SUMOylated XPC | 6790487 → 6790468 → 5689624 → 67443 |
| 76 | R-HSA-6797606 CDK12 phosphorylates RNA Pol II CTD at DNA repair genes | 6797606 → 6797614 → 6797611 → 109634 → 67443 |
| 77 | R-HSA-6797616 CCNK:CDK12 binds RNA Pol II at DNA repair genes | 6797616 → 6797611 → 109634 → 67443 |
| 78 | R-HSA-73758 Recruitment of RNA Polymerase I:RRN3 to the 45S pre-rRNA gene | 73758 → 109634 → 67443 |
| 79 | R-HSA-73769 Loss of RRN3 from RNA Polymerase I promoter escape complex | 73769 → 73716 → 109634 → 67443 |
| 80 | R-HSA-73946 Abortive initiation after formation of the first phosphodiester bond | 73946 → 109634 → 67443 |
| 81 | R-HSA-74986 Elongation of pre-rRNA transcript | 74986 → 73717 → 109634 → 67443 |
| 82 | R-HSA-74992 Dissociation of PTRF:RNA Polymerase I:pre-rRNA complex | 74992 → 109634 → 67443 |
| 83 | R-HSA-74993 PTRF binds the paused RNA Polymerase I complex | 74993 → 74979 → 73717 → 109634 → 67443 |
| 84 | R-HSA-74994 Elongating RNA Polymerase I Transcription Complex pauses at the TTF1:Sal Box | 74994 → 9988366 → 73717 → 109634 → 67443 |
| 85 | R-HSA-75850 Addition of the third nucleotide on the nascent transcript | 75850 → 109878 → 109634 → 67443 |
| 86 | R-HSA-75856 Abortive Initiation Before Second Transition | 75856 → 109634 → 67443 |
| 87 | R-HSA-75861 NTP Binds Active Site of RNA Polymerase II | 75861 → 109876 → 109634 → 67443 |
| 88 | R-HSA-75862 Fall Back to Closed Pre-initiation Complex | 75862 → 109876 → 109634 → 67443 |
| 89 | R-HSA-75864 Newly Formed Phosphodiester Bond Stabilized and PPi Released | 75864 → 83601 → 109634 → 67443 |
| 90 | R-HSA-75866 Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP | 75866 → 83601 → 109634 → 67443 |
| 91 | R-HSA-75869 Addition of the fourth nucleotide on the Nascent Transcript: Second Transition | 75869 → 75878 → 109634 → 67443 |
| 92 | R-HSA-75873 Addition of Nucleotides 5 through 9 on the growing Transcript | 75873 → 75881 → 109634 → 67443 |
| 93 | R-HSA-75891 Abortive Initiation After Second Transition | 75891 → 109634 → 67443 |
| 94 | R-HSA-75949 RNA Polymerase II Promoter Opening: First Transition | 75949 → 109635 → 109634 → 67443 |
| 95 | R-HSA-76576 Addition of nucleotides 10 and 11 on the growing transcript: Third Transition | 76576 → 75882 → 109634 → 67443 |
| 96 | R-HSA-77068 Activation of GT | 77068 → 77053 → 109634 → 67443 |
| 97 | R-HSA-77069 RNA Polymerase II CTD (phosphorylated) binds to CE | 77069 → 157174 → 109634 → 67443 |
| 98 | R-HSA-77071 Phosphorylation (Ser5) of RNA pol II CTD | 77071 → 157171 → 109634 → 67443 |
| 99 | R-HSA-77073 SPT5 subunit of Pol II binds the RNA triphosphatase (RTP) | 77073 → 77056 → 109634 → 67443 |
| 100 | R-HSA-77077 Capping complex formation | 77077 → 77061 → 109634 → 67443 |
| 101 | R-HSA-77078 Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme | 77078 → 77063 → 77061 → 109634 → 67443 |
| 102 | R-HSA-77081 Formation of the CE:GMP intermediate complex | 77081 → 77064 → 77061 → 109634 → 67443 |
| 103 | R-HSA-77083 Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA | 77083 → 77066 → 77061 → 109634 → 67443 |
| 104 | R-HSA-77085 Dissociation of transcript with 5'-GMP from GT | 77085 → 77066 → 77061 → 109634 → 67443 |
| 105 | R-HSA-77090 Methylation of GMP-cap by RNA Methyltransferase | 77090 → 109634 → 67443 |
| 106 | R-HSA-9613494 Unwinding of DNA for the Nascent Transcript: Second Transition | 9613494 → 75878 → 109634 → 67443 |
| 107 | R-HSA-9613497 Unwinding DNA for the nascent transcript | 9613497 → 109878 → 109634 → 67443 |
| 108 | R-HSA-9684118 ERCC3-facilitated RNA Pol II backtracking in TC-NER | 9684118 → 9684117 → 9684121 → 9684120 → 9684119 → 109634 → 67443 |
| 118 | R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER) | 6781827 → 6782234 → 109634 → 67443 |
| 144 | R-HSA-6782131 ERCC2-facilitated RNA Pol II backtracking in TC-NER | 6782131 → 6782120 → 67443 |
UniProt P18074 reports P18074-1, the 760-residue canonical protein, and P18074-2. The three recorded edits for P18074-2 delete canonical residues1–24, replace414–429 with QAQHCGSSRNQKRSHP, and delete430–760. Applying these explicit edits yields405 residues. This is a sequence reconstruction, not an assay of expression, stability, localization, catalytic activity or TFIIH incorporation. Patient-specific truncations and engineered K48R or other mutant constructs are separate experimental products.
Current GO:0035315 has direct epidermal-cell and neuron-differentiation parents. Its name alone does not establish the cell type relevant to the inaccessible TTD review. GO:0005669 denotes TFIID, whereas GO:0000439 describes the seven-subunit TFIIH core including XPD; PMID:27193682 explicitly used TBP in place of TFIID. The ATP-hydrolysis annotations retain the separately measured chemistry. The broad phosphorus-anhydride hydrolase annotation is refined to GO:0016887, whose current is_a ancestry includes GO:0016818; the directional helicase activity remains independently represented.
Follow-up original-source check: PMID:19934020 Results/Figure 5C and ATPase Methods independently support ATP hydrolysis by high-salt-washed human XPD preparations, with retained ATPase in variants that lose productive unwinding. The caption and Methods give different incubation durations, so no exact duration is asserted here. GO:0016887 identifies ATP hydrolysis and its Rhea:13065 reaction; its is_a ancestry contains the broad phosphorus-anhydride hydrolase term.