9IJJ image
Deposition Date 2024-06-23
Release Date 2025-06-04
Last Version Date 2025-09-10
Entry Detail
PDB ID:
9IJJ
Title:
In situ structure of the central apparatus in mouse sperm axoneme.
Biological Source:
Source Organism(s):
Mus musculus (Taxon ID: 10090)
Method Details:
Experimental Method:
Resolution:
7.70 Å
Aggregation State:
CELL
Reconstruction Method:
SUBTOMOGRAM AVERAGING
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Sperm acrosome-associated pro
Gene (Uniprot):Spaca9
Chain IDs:CM (auth: 1A), DM (auth: 1B), EM (auth: 1C), FM (auth: 1D), GM (auth: 1G), HM (auth: 1I), IM (auth: 1E), JM (auth: 1F), KM (auth: 1J), LM (auth: 1K), MM (auth: 1L), NM (auth: 1M), OM (auth: 1N), PM (auth: 1O), QM (auth: 1P), RM (auth: 1Q), SM (auth: 1R), TM (auth: 1S), UM (auth: 1T), VM (auth: 1U), WM (auth: 1V), XM (auth: 1W), YM (auth: 1X), ZM (auth: 1Y), AN (auth: 1Z), BN (auth: 1a), CN (auth: 1b), DN (auth: 1c), EN (auth: 1d), MP (auth: 2A), NP (auth: 2D), OP (auth: 2B), PP (auth: 2C), QP (auth: 2F), RP (auth: 2E), SP (auth: 2G), TP (auth: 2H), UP (auth: 2I), VP (auth: 2J), WP (auth: 2K), XP (auth: 2L), YP (auth: 2M), ZP (auth: 2N), AQ (auth: 2O), BQ (auth: 2P), CQ (auth: 2Q), DQ (auth: 2R), EQ (auth: 2S), FQ (auth: 2T), GQ (auth: 2U), HQ (auth: 2V), KQ (auth: 1e), LQ (auth: 1f), MQ (auth: 1g), NQ (auth: 1h), OQ (auth: 1i), PQ (auth: 1j), QQ (auth: 1k)
Chain Length:0
Number of Molecules:58
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Unknown1
Chain IDs:LN (auth: 3A)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Spermatogenesis-associated pr
Gene (Uniprot):Spata17
Chain IDs:MN (auth: 3B), TN (auth: 3C)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Calmodulin-1
Gene (Uniprot):Calm1
Chain IDs:UL (auth: 3D), NN (auth: 3E), ON (auth: 3F), PN (auth: 3G), UN (auth: 3H), VN (auth: 3I), WN (auth: 3J)
Chain Length:0
Number of Molecules:7
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap119
Chain IDs:QN (auth: 3K), RN (auth: 3L), XN (auth: 3M), YN (auth: 3N), AO (auth: 3O), BO (auth: 3P)
Chain Length:0
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:MORN repeat containing 2
Gene (Uniprot):Morn2
Chain IDs:SN (auth: 3Q), ZN (auth: 3R), CO (auth: 3S)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Protein dpy-30 homolog
Gene (Uniprot):Dpy30
Chain IDs:FN (auth: 3X), GN (auth: 3Y), HN (auth: 3V), IN (auth: 3W), JN (auth: 3T), KN (auth: 3U)
Chain Length:0
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Unknown2
Chain IDs:DO (auth: 3Z), EO (auth: 3a)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Unknown3
Chain IDs:FO (auth: 3b), GO (auth: 3c), HO (auth: 3d)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Unknown4
Chain IDs:IO (auth: 3e)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Unknown5
Chain IDs:JO (auth: 3f)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Unknown6
Chain IDs:KO (auth: 3g)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia and flagella-associated
Gene (Uniprot):Cfap47
Chain IDs:LO (auth: 4A), MO (auth: 4B)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Germ cell-less protein-like 1
Gene (Uniprot):Gmcl1
Chain IDs:SO (auth: 4C), TO (auth: 4D), UO (auth: 4E), VO (auth: 4F)
Chain Length:0
Number of Molecules:4
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Hydrocephalus-inducing protei
Gene (Uniprot):Hydin
Chain IDs:NO (auth: 4G), OO (auth: 4H), PO (auth: 4I), QO (auth: 4J), RO (auth: 4K)
Chain Length:0
Number of Molecules:5
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Sperm flagellar protein 2
Gene (Uniprot):Spef2
Chain IDs:WO (auth: 4M), YO (auth: 4N), AP (auth: 4L)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Leucine-rich repeat and guany
Gene (Uniprot):Lrguk
Chain IDs:XO (auth: 4P), ZO (auth: 4Q), BP (auth: 4O)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Putative aspartate aminotrans
Gene (Uniprot):Got1l1
Chain IDs:CP (auth: 4R), DP (auth: 4S), EP (auth: 4T), FP (auth: 4U), GP (auth: 4V), HP (auth: 4W)
Chain Length:0
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Leucine-rich repeat and death
Gene (Uniprot):Lrrd1
Chain IDs:IP (auth: 4X), JP (auth: 4Y)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:G protein-coupled receptor ki
Gene (Uniprot):Grk3
Chain IDs:KP (auth: 4Z)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein phos
Gene (Uniprot):Ppp1cc
Chain IDs:LP (auth: 4a)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Microtubule-associated protei
Gene (Uniprot):Map1s
Chain IDs:IQ (auth: 4b), JQ (auth: 4c)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Ankyrin repeat and MYND domai
Gene (Uniprot):Ankmy1
Chain IDs:UQ (auth: 5B)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Leucine-rich repeat-containin
Gene (Uniprot):Lrrc43
Chain IDs:VQ (auth: 5C)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia and flagella associated
Gene (Uniprot):Cfap46
Chain IDs:W (auth: A), X (auth: B)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap69
Chain IDs:ZL (auth: A2), AM (auth: A3), BM (auth: A4)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Sperm-associated antigen 6
Gene (Uniprot):Spag6
Chain IDs:XK (auth: AA), YK (auth: AB), ZK (auth: AC), AL (auth: AD), BL (auth: AE), CL (auth: AF), DL (auth: AG), EL (auth: AH), FL (auth: AI), GL (auth: AJ), HL (auth: AK), IL (auth: AL), JL (auth: AM), KL (auth: AN), LL (auth: AO), ML (auth: AP), NL (auth: AQ), OL (auth: AR), PL (auth: AS), QL (auth: AT), RL (auth: AU), SL (auth: AV), TL (auth: AW), VL (auth: AX), WL (auth: AY), XL (auth: AZ), YL (auth: A1)
Chain Length:0
Number of Molecules:27
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Tubulin beta-4B chain
Gene (Uniprot):Tubb4b
Chain IDs:XA (auth: Ab), ZA (auth: Ad), BB (auth: Af), DB (auth: Ah), FB (auth: Aj), HB (auth: Bb), JB (auth: Bd), LB (auth: Bf), NB (auth: Bh), PB (auth: Bj), RB (auth: Cb), TB (auth: Cd), VB (auth: Cf), XB (auth: Ch), ZB (auth: Cj), BC (auth: Db), DC (auth: Dd), FC (auth: Df), HC (auth: Dh), JC (auth: Dj), LC (auth: Eb), NC (auth: Ed), PC (auth: Ef), RC (auth: Eh), TC (auth: Ej), WC (auth: Fb), YC (auth: Fd), AD (auth: Ff), CD (auth: Fh), ED (auth: Fj), GD (auth: Gb), ID (auth: Gd), KD (auth: Gf), MD (auth: Gh), OD (auth: Gj), QD (auth: Hb), SD (auth: Hd), UD (auth: Hf), WD (auth: Hh), YD (auth: Hj), AE (auth: Ib), CE (auth: Id), EE (auth: If), GE (auth: Ih), IE (auth: Ij), KE (auth: Jb), ME (auth: Jd), OE (auth: Jf), QE (auth: Jh), SE (auth: Jj), TE (auth: Kb), VE (auth: Kd), XE (auth: Kf), ZE (auth: Kh), BF (auth: Kj), DF (auth: Lb), FF (auth: Ld), HF (auth: Lf), JF (auth: Lh), LF (auth: Lj), NF (auth: Mb), PF (auth: Md), RF (auth: Mf), TF (auth: Mh), VF (auth: Mj), XF (auth: An), ZF (auth: Ap), BG (auth: Ar), DG (auth: At), FG (auth: Av), HG (auth: Bn), JG (auth: Bp), LG (auth: Br), NG (auth: Bt), PG (auth: Bv), RG (auth: Cn), TG (auth: Cp), VG (auth: Cr), XG (auth: Ct), ZG (auth: Cv), BH (auth: Dn), DH (auth: Dp), FH (auth: Dr), HH (auth: Dt), JH (auth: Dv), LH (auth: En), NH (auth: Ep), PH (auth: Er), RH (auth: Et), TH (auth: Ev), WH (auth: Fp), YH (auth: Fr), AI (auth: Ft), CI (auth: Fv), EI (auth: Fn), GI (auth: Gp), II (auth: Gr), KI (auth: Gt), MI (auth: Gv), OI (auth: Gn), QI (auth: Hp), SI (auth: Hr), UI (auth: Ht), WI (auth: Hv), YI (auth: Hn), AJ (auth: Ip), CJ (auth: Ir), EJ (auth: It), GJ (auth: Iv), IJ (auth: In), KJ (auth: Jp), MJ (auth: Jr), OJ (auth: Jt), QJ (auth: Jv), SJ (auth: Jn), TJ (auth: Kn), VJ (auth: Kp), XJ (auth: Kr), ZJ (auth: Kt), BK (auth: Kv), DK (auth: Ln), FK (auth: Lp), HK (auth: Lr), JK (auth: Lt), LK (auth: Lv), NK (auth: Mn), PK (auth: Mp), RK (auth: Mr), TK (auth: Mt), VK (auth: Mv)
Chain Length:0
Number of Molecules:130
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Tubulin alpha-3 chain
Gene (Uniprot):Tuba3a, Tuba3b
Chain IDs:YA (auth: Ac), AB (auth: Ae), CB (auth: Ag), EB (auth: Ai), GB (auth: Ak), IB (auth: Bc), KB (auth: Be), MB (auth: Bg), OB (auth: Bi), QB (auth: Bk), SB (auth: Cc), UB (auth: Ce), WB (auth: Cg), YB (auth: Ci), AC (auth: Ck), CC (auth: Dc), EC (auth: De), GC (auth: Dg), IC (auth: Di), KC (auth: Dk), MC (auth: Ec), OC (auth: Ee), QC (auth: Eg), SC (auth: Ei), UC (auth: Ek), VC (auth: Fa), XC (auth: Fc), ZC (auth: Fe), BD (auth: Fg), DD (auth: Fi), FD (auth: Ga), HD (auth: Gc), JD (auth: Ge), LD (auth: Gg), ND (auth: Gi), PD (auth: Ha), RD (auth: Hc), TD (auth: He), VD (auth: Hg), XD (auth: Hi), ZD (auth: Ia), BE (auth: Ic), DE (auth: Ie), FE (auth: Ig), HE (auth: Ii), JE (auth: Ja), LE (auth: Jc), NE (auth: Je), PE (auth: Jg), RE (auth: Ji), UE (auth: Kc), WE (auth: Ke), YE (auth: Kg), AF (auth: Ki), CF (auth: Kk), EF (auth: Lc), GF (auth: Le), IF (auth: Lg), KF (auth: Li), MF (auth: Lk), OF (auth: Mc), QF (auth: Me), SF (auth: Mg), UF (auth: Mi), WF (auth: Mk), YF (auth: Ao), AG (auth: Aq), CG (auth: As), EG (auth: Au), GG (auth: Aw), IG (auth: Bo), KG (auth: Bq), MG (auth: Bs), OG (auth: Bu), QG (auth: Bm), SG (auth: Co), UG (auth: Cq), WG (auth: Cs), YG (auth: Cu), AH (auth: Cm), CH (auth: Do), EH (auth: Dq), GH (auth: Ds), IH (auth: Du), KH (auth: Dm), MH (auth: Eo), OH (auth: Eq), QH (auth: Es), SH (auth: Eu), UH (auth: Em), VH (auth: Fo), XH (auth: Fq), ZH (auth: Fs), BI (auth: Fu), DI (auth: Fw), FI (auth: Go), HI (auth: Gq), JI (auth: Gs), LI (auth: Gu), NI (auth: Gw), PI (auth: Ho), RI (auth: Hq), TI (auth: Hs), VI (auth: Hu), XI (auth: Hw), ZI (auth: Io), BJ (auth: Iq), DJ (auth: Is), FJ (auth: Iu), HJ (auth: Iw), JJ (auth: Jo), LJ (auth: Jq), NJ (auth: Js), PJ (auth: Ju), RJ (auth: Jw), UJ (auth: Ko), WJ (auth: Kq), YJ (auth: Ks), AK (auth: Ku), CK (auth: Km), EK (auth: Lo), GK (auth: Lq), IK (auth: Ls), KK (auth: Lu), MK (auth: Lm), OK (auth: Mo), QK (auth: Mq), SK (auth: Ms), UK (auth: Mu), WK (auth: Mm)
Chain Length:0
Number of Molecules:130
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap74
Chain IDs:Y (auth: C), Z (auth: D), AA (auth: E)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain containing
Gene (Uniprot):Ccdc180
Chain IDs:BA (auth: F), CA (auth: G)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap54
Chain IDs:DA (auth: H), EA (auth: I)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia and flagella associated
Gene (Uniprot):Cfap99
Chain IDs:RQ (auth: J), SQ (auth: K), TQ (auth: 5A)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap221
Chain IDs:FA (auth: L)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Leucine rich repeat containin
Gene (Uniprot):Lrrc72
Chain IDs:GA (auth: M)
Chain Length:0
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Deleted in lung and esophagea
Gene (Uniprot):Dlec1
Chain IDs:HA (auth: O), IA (auth: P)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Sperm-associated antigen 16 p
Gene (Uniprot):Spag16
Chain IDs:JA (auth: Q), KA (auth: R), LA (auth: S), MA (auth: T), NA (auth: U), OA (auth: V)
Chain Length:0
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Spermatogenesis-associated pr
Gene (Uniprot):Spata4
Chain IDs:A (auth: b), K (auth: a), PA (auth: W), QA (auth: X), RA (auth: Y), SA (auth: Z)
Chain Length:0
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Kinesin-like protein KIF9
Gene (Uniprot):Kif9
Chain IDs:B (auth: c), C (auth: d), D (auth: e), E (auth: f), F (auth: g)
Chain Length:0
Number of Molecules:5
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap65
Chain IDs:G (auth: h), H (auth: i), I (auth: j)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap70
Chain IDs:J (auth: k), L (auth: n), M (auth: o), N (auth: p), V (auth: m), WA (auth: l)
Chain Length:0
Number of Molecules:6
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Protein FAM228B
Gene (Uniprot):Fam228b
Chain IDs:O (auth: q), P (auth: r), Q (auth: s)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associate
Gene (Uniprot):Cfap20
Chain IDs:R (auth: t), S (auth: u)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:MYCBP-associated protein
Gene (Uniprot):Mycbpap
Chain IDs:T (auth: v), U (auth: w)
Chain Length:0
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Sperm-associated antigen 17
Gene (Uniprot):Spag17
Chain IDs:TA (auth: x), UA (auth: y), VA (auth: z)
Chain Length:0
Number of Molecules:3
Biological Source:Mus musculus
Ligand Molecules
Primary Citation
In situ structure of the mouse sperm central apparatus reveals mechanistic insights into asthenozoospermia.
Cell Res. 35 551 567 (2025)
PMID: 40473901 DOI: 10.1038/s41422-025-01135-2

Abstact

The central apparatus (CA) within the sperm axoneme is vital for sperm motility, yet its molecular architecture and functional mechanisms remain incompletely understood. Combining cryo-electron tomography and AlphaFold2, we resolved the in-cell structure of mouse sperm CA at a subnanometer resolution and built a near-complete atomic model. Our analysis identified 39 CA-associated proteins, including eight previously unreported components. By presenting the full-length structures of CFAP47 and HYDIN, we elucidate their molecular roles in tethering the C1 and C2 microtubules within the CA. Specifically, HYDIN forms a semicircular chain that encircles C1 and C2, with its N-terminal half driving the C1-C2 connection and its C-terminal half providing axial support in C2. CFAP47, the core structural component of the bridge, binds C1 through its N-terminal domains, interacts with HYDIN via its central CFAP47-ring, and anchors to C2 through its C-terminal region. The significantly reduced sperm motility and impaired CA structure observed in Cfap47-knockout mice confirmed the important role of CFAP47. Furthermore, genetic analysis of infertile Chinese men with asthenozoospermia identified previously unreported mutations in the CFAP47. The CA structural model elucidates the pathogenic mechanisms of these mutations, establishing a direct link between CFAP47 dysfunction and impaired sperm motility. Therefore, our study provides mechanistic insights into CA-related fertility disorders.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
Feedback Form
Name
Email
Institute
Feedback