8I7R image
Deposition Date 2023-02-02
Release Date 2023-10-11
Last Version Date 2023-12-06
Entry Detail
PDB ID:
8I7R
Keywords:
STRUCTURAL PROTEIN
Title:
In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
6.50 Å
Aggregation State:
CELL
Reconstruction Method:
SUBTOMOGRAM AVERAGING
8I7R validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Meiosis-specific nuclear structural protein 1
Gene (Uniprot):Mns1
Chain IDs:A, R (auth: B)
Chain Length:491
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:Q61884 Pfam ID:PF13868
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tektin-1
Gene (Uniprot):Tekt1
Chain IDs:B (auth: A1), C (auth: A2), D (auth: A3), E (auth: A4)
Chain Length:418
Number of Molecules:4
Biological Source:Mus musculus
UniProt ID:Q9DAJ2 Pfam ID:PF03148
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin beta-4B chain
Gene (Uniprot):Tubb4b
Chain IDs:F (auth: AB), H (auth: AD), J (auth: AF), L (auth: AH), N (auth: AJ), P (auth: AL), BA (auth: BB), DA (auth: BD), FA (auth: BF), HA (auth: BH), JA (auth: BJ), LA (auth: BL), XA (auth: CB), ZA (auth: CD), BB (auth: CF), DB (auth: CH), FB (auth: CJ), HB (auth: CL), YB (auth: DB), AC (auth: DD), CC (auth: DF), EC (auth: DH), GC (auth: DJ), IC (auth: DL), QC (auth: EB), SC (auth: ED), UC (auth: EF), WC (auth: EH), YC (auth: EJ), AD (auth: EL), MD (auth: FB), OD (auth: FD), QD (auth: FF), SD (auth: FH), UD (auth: FJ), WD (auth: FL), SE (auth: GB), UE (auth: GD), WE (auth: GF), YE (auth: GH), AF (auth: GJ), CF (auth: GL), LF (auth: HB), NF (auth: HD), PF (auth: HF), RF (auth: HH), TF (auth: HJ), VF (auth: HL), BG (auth: IB), DG (auth: ID), FG (auth: IF), HG (auth: IH), JG (auth: IJ), LG (auth: IL), SG (auth: JB), UG (auth: JD), WG (auth: JF), YG (auth: JH), AH (auth: JJ), CH (auth: JL), KH (auth: KB), MH (auth: KD), OH (auth: KF), QH (auth: KH), SH (auth: KJ), UH (auth: KL), BI (auth: LB), DI (auth: LD), FI (auth: LF), HI (auth: LH), JI (auth: LJ), LI (auth: LL), QI (auth: MB), SI (auth: MD), UI (auth: MF), WI (auth: MH), YI (auth: MJ), AJ (auth: ML), IJ (auth: NB), KJ (auth: ND), MJ (auth: NF), OJ (auth: NH), QJ (auth: NJ), SJ (auth: NL), YJ (auth: OB), AK (auth: OD), CK (auth: OF), EK (auth: OH), GK (auth: OJ), IK (auth: OL), OK (auth: PB), QK (auth: PD), SK (auth: PF), UK (auth: PH), WK (auth: PJ), YK (auth: PL), EL (auth: QB), GL (auth: QD), IL (auth: QF), KL (auth: QH), ML (auth: QJ), OL (auth: QL), UL (auth: RB), WL (auth: RD), YL (auth: RF), AM (auth: RH), CM (auth: RJ), EM (auth: RL), HM (auth: SB), JM (auth: SD), LM (auth: SF), NM (auth: SH), PM (auth: SJ), RM (auth: SL), UM (auth: TB), WM (auth: TD), YM (auth: TF), AN (auth: TH), CN (auth: TJ), EN (auth: TL), GN (auth: TN), JN (auth: UB), LN (auth: UD), NN (auth: UF), PN (auth: UH), RN (auth: UJ), TN (auth: UL), WN (auth: VB), YN (auth: VD), AO (auth: VF), CO (auth: VH), EO (auth: VJ), GO (auth: VL), JO (auth: WB), LO (auth: WD), NO (auth: WF), PO (auth: WH), RO (auth: WJ), TO (auth: WL)
Chain Length:427
Number of Molecules:139
Biological Source:Mus musculus
UniProt ID:P68372 Pfam ID:PF00091, PF03953
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Detyrosinated tubulin alpha-3 chain
Gene (Uniprot):Tuba3a, Tuba3b
Chain IDs:G (auth: AC), I (auth: AE), K (auth: AG), M (auth: AI), O (auth: AK), Q (auth: AM), CA (auth: BC), EA (auth: BE), GA (auth: BG), IA (auth: BI), KA (auth: BK), MA (auth: BM), YA (auth: CC), AB (auth: CE), CB (auth: CG), EB (auth: CI), GB (auth: CK), IB (auth: CM), XB (auth: DA), ZB (auth: DC), BC (auth: DE), DC (auth: DG), FC (auth: DI), HC (auth: DK), PC (auth: EA), RC (auth: EC), TC (auth: EE), VC (auth: EG), XC (auth: EI), ZC (auth: EK), LD (auth: FA), ND (auth: FC), PD (auth: FE), RD (auth: FG), TD (auth: FI), VD (auth: FK), RE (auth: GA), TE (auth: GC), VE (auth: GE), XE (auth: GG), ZE (auth: GI), BF (auth: GK), KF (auth: HA), MF (auth: HC), OF (auth: HE), QF (auth: HG), SF (auth: HI), UF (auth: HK), AG (auth: IA), CG (auth: IC), EG (auth: IE), GG (auth: IG), IG (auth: II), KG (auth: IK), MG (auth: IM), RG (auth: JA), TG (auth: JC), VG (auth: JE), XG (auth: JG), ZG (auth: JI), BH (auth: JK), JH (auth: KA), LH (auth: KC), NH (auth: KE), PH (auth: KG), RH (auth: KI), TH (auth: KK), AI (auth: LA), CI (auth: LC), EI (auth: LE), GI (auth: LG), II (auth: LI), KI (auth: LK), RI (auth: MC), TI (auth: ME), VI (auth: MG), XI (auth: MI), ZI (auth: MK), BJ (auth: MM), HJ (auth: NA), JJ (auth: NC), LJ (auth: NE), NJ (auth: NG), PJ (auth: NI), RJ (auth: NK), XJ (auth: OA), ZJ (auth: OC), BK (auth: OE), DK (auth: OG), FK (auth: OI), HK (auth: OK), NK (auth: PA), PK (auth: PC), RK (auth: PE), TK (auth: PG), VK (auth: PI), XK (auth: PK), ZK (auth: PM), FL (auth: QC), HL (auth: QE), JL (auth: QG), LL (auth: QI), NL (auth: QK), PL (auth: QM), VL (auth: RC), XL (auth: RE), ZL (auth: RG), BM (auth: RI), DM (auth: RK), FM (auth: RM), IM (auth: SC), KM (auth: SE), MM (auth: SG), OM (auth: SI), QM (auth: SK), SM, VM (auth: TC), XM (auth: TE), ZM (auth: TG), BN (auth: TI), DN (auth: TK), FN (auth: TM), IN (auth: UA), KN (auth: UC), MN (auth: UE), ON (auth: UG), QN (auth: UI), SN (auth: UK), VN (auth: VA), XN (auth: VC), ZN (auth: VE), BO (auth: VG), DO (auth: VI), FO (auth: VK), IO (auth: WA), KO (auth: WC), MO (auth: WE), OO (auth: WG), QO (auth: WI), SO (auth: WK)
Chain Length:438
Number of Molecules:140
Biological Source:Mus musculus
UniProt ID:P05214 Pfam ID:PF00091, PF03953
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tektin-2
Gene (Uniprot):Tekt2
Chain IDs:S (auth: B1), T (auth: B2), U (auth: B3), V (auth: B4), W (auth: B5), X (auth: B6), Y (auth: B7), Z (auth: B8), AA (auth: B9)
Chain Length:430
Number of Molecules:9
Biological Source:Mus musculus
UniProt ID:Q922G7 Pfam ID:PF03148
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleoside diphosphate kinase 7
Gene (Uniprot):Nme7
Chain IDs:NA (auth: C), NB (auth: D)
Chain Length:395
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:Q9QXL8 Pfam ID:PF00334
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tektin-3
Gene (Uniprot):Tekt3
Chain IDs:OA (auth: C1), PA (auth: C2), QA (auth: C3), RA (auth: C4), SA (auth: C5), TA (auth: C6), UA (auth: C7), VA (auth: C8), WA (auth: C9), JB (auth: Ca), KB (auth: Cb), LB (auth: Cc), MB (auth: Cd)
Chain Length:490
Number of Molecules:13
Biological Source:Mus musculus
UniProt ID:Q6X6Z7 Pfam ID:PF03148
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tektin-4
Gene (Uniprot):Tekt4
Chain IDs:OB (auth: D1), PB (auth: D2), QB (auth: D3), RB (auth: D4), SB (auth: D5), TB (auth: D6), UB (auth: D7), VB (auth: D8), WB (auth: D9), JC (auth: Da)
Chain Length:447
Number of Molecules:10
Biological Source:Mus musculus
UniProt ID:Q149S1 Pfam ID:PF03148
Protein Blast
Polymer Type:polypeptide(L)
Molecule:EF-hand domain-containing family member B
Gene (Uniprot):Efhb
Chain IDs:KC (auth: E), BD (auth: F)
Chain Length:853
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:Q8CDU5 Pfam ID:PF13499
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tektin bundle-interacting protein 1
Gene (Uniprot):Tektip1
Chain IDs:LC (auth: E1), MC (auth: E2), NC (auth: E3), OC (auth: E4)
Chain Length:206
Number of Molecules:4
Biological Source:Mus musculus
UniProt ID:A6H6Q4 Pfam ID:PF15041
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tektin-5
Gene (Uniprot):Tekt5
Chain IDs:CD (auth: F1), DD (auth: F2), ED (auth: F3), FD (auth: F4), GD (auth: F5), HD (auth: F6), ID (auth: F7), JD (auth: F8), KD (auth: F9), XD (auth: Fa), YD (auth: Fb), ZD (auth: Fc), AE (auth: Fd), BE (auth: Fe), CE (auth: Ff), DE (auth: Fg), EE (auth: Fh), FE (auth: Fi), GE (auth: Fj), HE (auth: Fk), IE (auth: Fl), JE (auth: Fm)
Chain Length:557
Number of Molecules:22
Biological Source:Mus musculus
UniProt ID:G5E8A8 Pfam ID:PF03148
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 53
Gene (Uniprot):Cfap53
Chain IDs:KE (auth: G), DF (auth: H)
Chain Length:514
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:Q9D439 Pfam ID:PF13868
Protein Blast
Polymer Type:polypeptide(L)
Molecule:EF-hand domain-containing protein 1
Gene (Uniprot):Efhc1
Chain IDs:LE (auth: G1), ME (auth: G2), NE (auth: G3)
Chain Length:648
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q9D9T8 Pfam ID:PF06565, PF13499
Protein Blast
Polymer Type:polypeptide(L)
Molecule:EF-hand domain-containing family member C2
Gene (Uniprot):Efhc2
Chain IDs:OE (auth: G4), PE (auth: G5), QE (auth: G6)
Chain Length:750
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q9D485 Pfam ID:PF06565
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein FAM166A
Gene (Uniprot):Cimip2a
Chain IDs:EF (auth: H1), FF (auth: H2), GF (auth: H3), HF (auth: H4), IF (auth: H5), JF (auth: H6)
Chain Length:319
Number of Molecules:6
Biological Source:Mus musculus
UniProt ID:Q9D4K5 Pfam ID:PF10629
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 95
Gene (Uniprot):Cfap95
Chain IDs:WF (auth: I)
Chain Length:228
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9CQC3 Pfam ID:PF15139
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein FAM166C
Gene (Uniprot):Cimip2c
Chain IDs:XF (auth: I1), YF (auth: I2), ZF (auth: I3)
Chain Length:200
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q9DAS2 Pfam ID:PF10629
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 107
Gene (Uniprot):Cfap107
Chain IDs:NG (auth: J)
Chain Length:196
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q4KKZ1 Pfam ID:PF22595
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dual specificity phosphatase 21
Gene (Uniprot):Dusp21
Chain IDs:OG (auth: J1), PG (auth: J2), QG (auth: J3)
Chain Length:189
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q9D9D8 Pfam ID:PF00782
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 161
Gene (Uniprot):Cfap161
Chain IDs:DH (auth: K), VH (auth: L)
Chain Length:303
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:Q6P8Y0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing protein 105
Gene (Uniprot):Tektl1
Chain IDs:EH (auth: K1), FH (auth: K2), GH (auth: K3), HH (auth: K4), IH (auth: K5)
Chain Length:499
Number of Molecules:5
Biological Source:Mus musculus
UniProt ID:Q9D4K7 Pfam ID:PF03148
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Enkurin
Gene (Uniprot):Enkur
Chain IDs:WH (auth: L1), XH (auth: L2), YH (auth: L3), ZH (auth: L4)
Chain Length:255
Number of Molecules:4
Biological Source:Mus musculus
UniProt ID:Q6SP97 Pfam ID:PF13864
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Piercer of microtubule wall 1 protein
Gene (Uniprot):Pierce1
Chain IDs:MI (auth: M)
Chain Length:167
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q5BN45 Pfam ID:PF14892
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Testis-expressed protein 43
Gene (Uniprot):Spmip10
Chain IDs:NI (auth: M1), OI (auth: M2), PI (auth: M3)
Chain Length:141
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q9D9I1 Pfam ID:PF14983
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Piercer of microtubule wall 2 protein
Gene (Uniprot):Pierce2
Chain IDs:CJ (auth: N)
Chain Length:122
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:V9GXK1 Pfam ID:PF14892
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 276
Gene (Uniprot):Cfap276
Chain IDs:DJ (auth: N1), EJ (auth: N2), FJ (auth: N3), GJ (auth: N4)
Chain Length:168
Number of Molecules:4
Biological Source:Mus musculus
UniProt ID:Q9DAD0 Pfam ID:PF12494
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RIB43A-like with coiled-coils protein 2
Gene (Uniprot):Ribc2
Chain IDs:TJ (auth: O), JK (auth: P), AL (auth: Q), QL (auth: R)
Chain Length:377
Number of Molecules:4
Biological Source:Mus musculus
UniProt ID:Q9D4Q1 Pfam ID:PF05914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein Flattop
Gene (Uniprot):Cfap126
Chain IDs:UJ (auth: O1), VJ (auth: O2), WJ (auth: O3)
Chain Length:189
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q6P8X9 Pfam ID:PF22611
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 52
Gene (Uniprot):Cfap52
Chain IDs:KK (auth: P1), LK (auth: P2), MK (auth: P3)
Chain Length:620
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q5F201 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:EF-hand calcium-binding domain-containing protein 6
Gene (Uniprot):Efcab6
Chain IDs:BL (auth: Q1), CL (auth: Q2), DL (auth: Q3)
Chain Length:1516
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:Q6P1E8 Pfam ID:PF13202, PF13833, PF08976, PF13499
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia and flagella-associated protein 77
Gene (Uniprot):Cfap77
Chain IDs:RL (auth: R1), SL (auth: R2), TL (auth: R3)
Chain Length:283
Number of Molecules:3
Biological Source:Mus musculus
UniProt ID:A0A087WRI3 Pfam ID:PF14825
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sperm-associated antigen 8
Gene (Uniprot):Spag8
Chain IDs:GM (auth: S), TM (auth: T)
Chain Length:470
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:Q3V0Q6 Pfam ID:PF22584
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 45
Gene (Uniprot):Cfap45
Chain IDs:HN (auth: U), UN (auth: V), HO (auth: W), UO (auth: X)
Chain Length:551
Number of Molecules:4
Biological Source:Mus musculus
UniProt ID:Q9D9U9 Pfam ID:PF13868
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 20
Gene (Uniprot):Cfap20
Chain IDs:VO (auth: XA), WO (auth: XB), XO (auth: XC), YO (auth: XD), ZO (auth: XE), AP (auth: XF), BP (auth: XG)
Chain Length:193
Number of Molecules:7
Biological Source:Mus musculus
UniProt ID:Q8BTU1 Pfam ID:PF05018
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Parkin coregulated gene protein homolog
Gene (Uniprot):Pacrg
Chain IDs:CP (auth: XH), DP (auth: XI), EP (auth: XJ), FP (auth: XK), GP (auth: XL), HP (auth: XM)
Chain Length:241
Number of Molecules:6
Biological Source:Mus musculus
UniProt ID:Q9DAK2 Pfam ID:PF10274
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 210
Gene (Uniprot):Cfap210
Chain IDs:IP (auth: Y), GQ (auth: Z)
Chain Length:547
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:A0JLY1 Pfam ID:PF13868
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sperm acrosome-associated protein 9
Gene (Uniprot):Spaca9
Chain IDs:JP (auth: YA), KP (auth: YB), LP (auth: YC), MP (auth: YD), NP (auth: YE), OP (auth: YF), PP (auth: YG), QP (auth: YH), RP (auth: YI), SP (auth: YJ), TP (auth: YK), UP (auth: YL), VP (auth: YM), WP (auth: YN), XP (auth: YO), YP, ZP (auth: YQ), AQ (auth: YR), BQ (auth: YS), CQ (auth: YT), DQ (auth: YU), EQ (auth: YV), FQ (auth: YW)
Chain Length:168
Number of Molecules:23
Biological Source:Mus musculus
UniProt ID:Q7TPM5 Pfam ID:PF15120
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cilia- and flagella-associated protein 141
Gene (Uniprot):Cfap141
Chain IDs:HQ (auth: a)
Chain Length:491
Number of Molecules:1
Biological Source:Mus musculus
UniProt ID:Q9D9D9 Pfam ID:PF15104
Ligand Molecules
GTP
Primary Citation
In-cell structural insight into the stability of sperm microtubule doublet.
Cell Discov 9 116 116 (2023)
PMID: 37989994 DOI: 10.1038/s41421-023-00606-3

Abstact

The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8I7R