DNAH3 (dynein axonemal heavy chain 3) is a 4116-residue heavy chain of a single-headed inner dynein arm (IDA). It has an N-terminal stem that anchors it in the axoneme and binds light intermediate chain, and a C-terminal motor head of six AAA+ modules with a coiled-coil stalk and microtubule-binding domain that generates minus-end-directed force between doublet microtubules. Cryo-EM of human respiratory axonemes identifies DNAH3 as the heavy chain of IDAc. DNAH3 is expressed mainly in testis and trachea; in the testis it is cytoplasmic in spermatogonia and spermatocytes and moves into the flagellum of developing spermatids. In sperm, DNAH3 forms a complex with the IDA light intermediate chain DNALI1 through its stem domain, and it is needed for the IDA heavy chains DNAH1, DNAH6 and DNAH10 and for DNALI1 to accumulate in the flagellum, while outer arm proteins are unaffected. Biallelic DNAH3 variants cause male infertility with asthenoteratozoospermia or MMAF, with IDA loss and, in some reports, central-pair, mitochondrial sheath and fibrous sheath defects. Dnah3 knockout male mice are infertile with severely reduced sperm motility and IDA loss; one knockout line was reported to have morphologically normal sperm with disturbed energy metabolism instead. Respiratory and ependymal cilia of Dnah3 knockout mice appear grossly normal and patients have not been reported with primary ciliary dyskinesia. ICSI overcomes the infertility in patients and mice.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003777 microtubule motor activity | NAS PMID:9256245 Isolation of several human axonemal dynein heavy chain genes... | TOO GENERAL | Summary: Author statement that dynein heavy chains are motor ATPases. Reason: True but uninformative: minus-end-directed microtubule motor activity (GO:0008569), ACCEPTed in this review by IBA and IEA, is_a microtubule motor activity and entails it. GO:0008569 is the core function. Supporting Evidence: PMID:9256245 Dynein heavy chains (DHCs) are the main components of multisubunit motor ATPase complexes called dyneins. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binding from InterPro; P-loops are retained in AAA1-AAA4. Reason: Correct but uninformative relative to the motor activity term. |
| GO:0005737 cytoplasm | IDA PMID:39503742 DNAH3 deficiency causes flagellar inner dynein arm loss and ... | KEEP AS NON CORE | Summary: Immunostaining of testis sections shows DNAH3 in the cytoplasm of spermatogonia and spermatocytes. Reason: Accurate experimental localization of a pre-assembly pool, presumably before transport into the flagellum; the functional site is the axoneme. Supporting Evidence: PMID:39503742 Initially, DNAH3 was expressed in the cytoplasm of spermatogonia and spermatocytes, and then it clearly transferred into the flagellum of early and late spermatids. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Combined automated cytoplasm annotation. Reason: DNAH3 is cytoplasmic in spermatogonia and spermatocytes before entering the flagellum, so the term is correct for a pre-assembly pool but is not where it functions. Supporting Evidence: PMID:39503742 Initially, DNAH3 was expressed in the cytoplasm of spermatogonia and spermatocytes, and then it clearly transferred into the flagellum of early and late spermatids. |
| GO:0005858 axonemal dynein complex | NAS PMID:9256245 Isolation of several human axonemal dynein heavy chain genes... | MODIFY | Summary: Author statement that the cloned gene is an axonemal dynein heavy chain. Reason: Correct but less specific than inner dynein arm, established by cryo-EM. Proposed replacements: inner dynein arm Supporting Evidence: PMID:37258679 IDAc is DNAH3 |
| GO:0005930 axoneme | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping (cilium axoneme). Reason: DNAH3 is an axonemal IDA heavy chain (IDAc). Supporting Evidence: PMID:37258679 IDAc is DNAH3 |
| GO:0007018 microtubule-based movement | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping to microtubule-based movement. Reason: True but uninformative: cilium movement involved in cell motility (GO:0060294), ACCEPTed in this review, is_a cilium movement, which is_a microtubule-based movement, and so entails it. |
| GO:0007288 sperm axoneme assembly | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of sperm axoneme assembly. Reason: Consistent with the IMP annotation from PMID:38312775. |
| GO:0007288 sperm axoneme assembly | IMP PMID:38312775 Bi-allelic variants in DNAH3 cause male infertility with ast... | ACCEPT | Summary: Patients with biallelic DNAH3 variants show loss of the central pair, partial absence of inner dynein arms and dislocated mitochondrial and fibrous sheaths; two Dnah3 knockout lines have asthenoteratozoospermia. Reason: Two independent groups report axonemal defects; inner dynein arm assembly is the more specific process, but sperm axoneme assembly is also correct. Supporting Evidence: PMID:38312775 TEM and immunostaining further showed the loss of the central pair of microtubules, a dislocated mitochondrial sheath and fibrous sheath, as well as a partial absence of the inner dynein arms |
| GO:0008569 minus-end-directed microtubule motor activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of minus-end-directed microtubule motor activity. Reason: DNAH3 retains a full-length dynein motor (AAA1-AAA6, stalk); no evidence of loss of motor function. Core molecular function. Supporting Evidence: file:human/DNAH3/DNAH3-uniprot.txt Produces force towards the minus ends of microtubules. |
| GO:0008569 minus-end-directed microtubule motor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro mapping of minus-end-directed microtubule motor activity. Reason: Consistent with the IBA. |
| GO:0030286 dynein complex | IEA GO_REF:0000002 | MODIFY | Summary: InterPro mapping to dynein complex. Reason: Too general; DNAH3 is an inner dynein arm heavy chain. Proposed replacements: inner dynein arm Supporting Evidence: PMID:37258679 IDAc is DNAH3 |
| GO:0031514 motile cilium | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt flagellum location mapped to motile cilium. Reason: DNAH3 is in the sperm flagellum and respiratory cilia. |
| GO:0036126 sperm flagellum | IDA PMID:39503742 DNAH3 deficiency causes flagellar inner dynein arm loss and ... | ACCEPT | Summary: Immunostaining shows DNAH3 in the flagellum of spermatids and sperm, lost in patients and knockout mice. Reason: Direct localization; core location. Supporting Evidence: PMID:39503742 These variants contributed to deficient DNAH3 expression in the patients' sperm flagella. |
| GO:0036126 sperm flagellum | IDA PMID:39588341 Novel bi-allelic DNAH3 variants cause oligoasthenoteratozoos... | ACCEPT | Summary: Immunofluorescence of sperm from controls and two patients was used to assess DNAH3 localization and expression. Reason: Independent confirmation of flagellar localization. Supporting Evidence: PMID:39588341 We performed immunofluorescence staining on sperm smears of healthy individuals and two patients to assess localization and expression changes of DNAH3, DNALI1, and COXIV. |
| GO:0036126 sperm flagellum | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of sperm flagellum localization. Reason: Consistent with the IDA annotations. |
| GO:0036156 inner dynein arm | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of inner dynein arm membership. Reason: Core component: cryo-EM identifies DNAH3 as the IDAc heavy chain. Supporting Evidence: PMID:37258679 IDAc is DNAH3 |
| GO:0036159 inner dynein arm assembly | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBD at PTN008951089 seeded by DNAH3 itself, DNAH7 and a mouse IDA heavy chain. Reason: DNAH3 does part of the work of IDA assembly as a structural heavy chain that binds DNALI1; its loss removes other IDA subunits from sperm. Supporting Evidence: PMID:41731497 our findings suggest that the interaction between DNAH3 and DNALI1 is critical for flagellum assembly |
| GO:0036159 inner dynein arm assembly | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of inner dynein arm assembly. Reason: Consistent with IMP and IBA. |
| GO:0036159 inner dynein arm assembly | IMP PMID:39503742 DNAH3 deficiency causes flagellar inner dynein arm loss and ... | ACCEPT | Summary: Loss of DNAH3 in patients and knockout mice reduces the IDA proteins DNAH1, DNAH6 and DNALI1 in sperm flagella, with abnormal IDA structure. Reason: Core process. Replicated by an independent knockout showing absence of IDAs and reduced DNAH6, DNAH10 and DNALI1 (PMID:41731497). Supporting Evidence: PMID:39503742 Moreover, the absence of DNAH3 led to decreased expression of other IDA-associated proteins, including DNAH1, DNAH6 and DNALI1. |
| GO:0045505 dynein intermediate chain binding | IBA GO_REF:0000033 | UNDECIDED | Summary: Family-level PAINT inference of dynein intermediate chain binding. Reason: IDAc is a single-headed inner arm; no intermediate chain partner of DNAH3 has been reported. The co-IP/MS study of DNAH3 identified DNALI1, a light intermediate chain. The IBD is seeded only by a cytoplasmic dynein, so this is left UNDECIDED. Propagation Review Root cause: UNRESOLVED Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000743491 UNRESOLVED Deep dynein heavy chain node spanning cytoplasmic and axonemal dyneins; the dynein intermediate chain binding IBD is seeded only by a Dictyostelium cytoplasmic dynein heavy chain. dictyBase:DDB_G0276355 SUPPORTS SOURCE BUT NOT TARGET Cytoplasmic dynein heavy chain; intermediate chain binding is well established there but single-headed axonemal inner arms are not known to carry intermediate chains. |
| GO:0045505 dynein intermediate chain binding | IEA GO_REF:0000002 | UNDECIDED | Summary: InterPro family mapping of dynein intermediate chain binding. Reason: Same considerations as the IBA. |
| GO:0051959 dynein light intermediate chain binding | IBA GO_REF:0000033 | ACCEPT | Summary: Family-level PAINT inference of dynein light intermediate chain binding. Reason: Directly supported: DNAH3 co-immunoprecipitates with DNALI1 from testis and the DNAH3 stem domain binds DNALI1 in co-transfection. Supporting Evidence: PMID:41731497 Further in vitro Co-IP assays validated that the DNAH3 Stem domain indeed mediates the interaction with DNALI1 |
| GO:0051959 dynein light intermediate chain binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro family mapping of dynein light intermediate chain binding. Reason: Supported by direct DNAH3-DNALI1 interaction data. Supporting Evidence: PMID:41731497 Combined comparative proteomics and co-immunoprecipitation analyses demonstrated that DNAH3 forms a complex with DNALI1. |
| GO:0060285 cilium-dependent cell motility | NAS PMID:9256245 Isolation of several human axonemal dynein heavy chain genes... | MODIFY | Summary: Non-traceable author statement from the 1997 cloning paper that axonemal dyneins drive ciliary and flagellar motility. Reason: Cell motility via a cilium applies to sperm; the specific term flagellated sperm motility is directly supported by knockout mice and patients. Proposed replacements: flagellated sperm motility Supporting Evidence: PMID:39774634 The sperm motility of Dnah3-knockout mice significantly declined compared to wild-type mice. |
| GO:0060294 cilium movement involved in cell motility | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBD at PTN000743491, where DNAH3 (Q8TD57) is among the seeds. Reason: DNAH3 drives sperm flagellar beating; knockout mice and patients have severely reduced sperm motility. DNAH3 appearing among the IBD sources reflects its own experimental grounding. Supporting Evidence: PMID:38312775 DNAH3 is a novel candidate causative gene for AT and is essential for sperm flagellar assembly and sperm motility in humans and mice |
| GO:0097729 9+2 motile cilium | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of 9+2 motile cilium localization. Reason: DNAH3 is the IDAc heavy chain in human respiratory axonemes and is present in sperm flagella, both 9+2 motile cilia. Supporting Evidence: PMID:37258679 IDAc is DNAH3 |
| GO:0120316 sperm flagellum assembly | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of sperm flagellum assembly. Reason: DNAH3 loss causes MMAF in patients and abnormal flagella in knockout mice. Supporting Evidence: PMID:38312775 we suggest that DNAH3 plays a major role in the assembly of sperm flagella in humans and mice |
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Download this section (compressed HTML)Q: Why do Dnah3 knockout lines differ in sperm morphology? Two studies report MMAF-like flagellar defects and IDA loss, while another reports normal sperm morphology with disturbed energy metabolism (PMID:39774634). Do allele position, genetic background or residual truncated protein explain this?
Q: DNAH3 is the IDAc heavy chain in human respiratory axonemes, yet Dnah3 knockout airway cilia look normal and patients lack PCD. Is IDAc dispensable for airway ciliary beating, or is its loss compensated?
Experiment: High-speed video and cryo-ET of airway cilia from Dnah3 knockout mice to test for subtle waveform changes and to confirm IDAc loss in situ.
Type: ciliary beat analysis and cryo-electron tomography
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