› 8i7r

Electron Microscopy
6.5Å resolution

In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat

Released:
DOI: 10.2210/pdb8i7r/pdb
PDB entry 8i7r coloured by chain, front view.
PDB entry 8i7r coloured by chain, side view.
PDB entry 8i7r coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
In-cell structural insight into the stability of sperm microtubule doublet.
Tai L, Yin G, Huang X, Sun F, Zhu Y
Cell Discov 9 116 (2023)
PMID: 37989994
Related structures: EMD-35230

Function and Biology Details

Reactions catalysed: 
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 450-mer (preferred)
PDBe Complex ID:
PDB-CPX-231514 (preferred)
Entry contents:
38 distinct polypeptide molecules
Macromolecules (38 distinct):
Meiosis-specific nuclear structural protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 491 amino acids
Theoretical weight: 60.35 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q61884 (Residues: 1-491; Coverage: 100%)
Gene name: Mns1
Sequence domains: Trichohyalin-plectin-homology domain
Tektin-1 Chains: A1, A2, A3, A4
Molecule details ›
Chains: A1, A2, A3, A4
Length: 418 amino acids
Theoretical weight: 48.71 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DAJ2 (Residues: 1-418; Coverage: 100%)
Gene name: Tekt1
Sequence domains: Tektin family
Tubulin beta-4B chain Chains: AB, AD, AF, AH, AJ, AL, BB, BD, BF, BH, BJ, BL, CB, CD, CF, CH, CJ, CL, DB, DD, DF, DH, DJ, DL, EB, ED, EF, EH, EJ, EL, FB, FD, FF, FH, FJ, FL, GB, GD, GF, GH, GJ, GL, HB, HD, HF, HH, HJ, HL, IB, ID, IF, IH, IJ, IL, JB, JD, JF, JH, JJ, JL, KB, KD, KF, KH, KJ, KL, LB, LD, LF, LH, LJ, LL, MB, MD, MF, MH, MJ, ML, NB, ND, NF, NH, NJ, NL, OB, OD, OF, OH, OJ, OL, PB, PD, PF, PH, PJ, PL, QB, QD, QF, QH, QJ, QL, RB, RD, RF, RH, RJ, RL, SB, SD, SF, SH, SJ, SL, TB, TD, TF, TH, TJ, TL, TN, UB, UD, UF, UH, UJ, UL, VB, VD, VF, VH, VJ, VL, WB, WD, WF, WH, WJ, WL
Molecule details ›
Chains: AB, AD, AF, AH, AJ, AL, BB, BD, BF, BH, BJ, BL, CB, CD, CF, CH, CJ, CL, DB, DD, DF, DH, DJ, DL, EB, ED, EF, EH, EJ, EL, FB, FD, FF, FH, FJ, FL, GB, GD, GF, GH, GJ, GL, HB, HD, HF, HH, HJ, HL, IB, ID, IF, IH, IJ, IL, JB, JD, JF, JH, JJ, JL, KB, KD, KF, KH, KJ, KL, LB, LD, LF, LH, LJ, LL, MB, MD, MF, MH, MJ, ML, NB, ND, NF, NH, NJ, NL, OB, OD, OF, OH, OJ, OL, PB, PD, PF, PH, PJ, PL, QB, QD, QF, QH, QJ, QL, RB, RD, RF, RH, RJ, RL, SB, SD, SF, SH, SJ, SL, TB, TD, TF, TH, TJ, TL, TN, UB, UD, UF, UH, UJ, UL, VB, VD, VF, VH, VJ, VL, WB, WD, WF, WH, WJ, WL
Length: 427 amino acids
Theoretical weight: 47.9 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P68372 (Residues: 1-427; Coverage: 96%)
Gene names: Tubb2c, Tubb4b
Sequence domains:
Tubulin alpha-3 chain Chains: AC, AE, AG, AI, AK, AM, BC, BE, BG, BI, BK, BM, CC, CE, CG, CI, CK, CM, DA, DC, DE, DG, DI, DK, EA, EC, EE, EG, EI, EK, FA, FC, FE, FG, FI, FK, GA, GC, GE, GG, GI, GK, HA, HC, HE, HG, HI, HK, IA, IC, IE, IG, II, IK, IM, JA, JC, JE, JG, JI, JK, KA, KC, KE, KG, KI, KK, LA, LC, LE, LG, LI, LK, MC, ME, MG, MI, MK, MM, NA, NC, NE, NG, NI, NK, OA, OC, OE, OG, OI, OK, PA, PC, PE, PG, PI, PK, PM, QC, QE, QG, QI, QK, QM, RC, RE, RG, RI, RK, RM, SC, SE, SG, SI, SK, SM, TC, TE, TG, TI, TK, TM, UA, UC, UE, UG, UI, UK, VA, VC, VE, VG, VI, VK, WA, WC, WE, WG, WI, WK
Molecule details ›
Chains: AC, AE, AG, AI, AK, AM, BC, BE, BG, BI, BK, BM, CC, CE, CG, CI, CK, CM, DA, DC, DE, DG, DI, DK, EA, EC, EE, EG, EI, EK, FA, FC, FE, FG, FI, FK, GA, GC, GE, GG, GI, GK, HA, HC, HE, HG, HI, HK, IA, IC, IE, IG, II, IK, IM, JA, JC, JE, JG, JI, JK, KA, KC, KE, KG, KI, KK, LA, LC, LE, LG, LI, LK, MC, ME, MG, MI, MK, MM, NA, NC, NE, NG, NI, NK, OA, OC, OE, OG, OI, OK, PA, PC, PE, PG, PI, PK, PM, QC, QE, QG, QI, QK, QM, RC, RE, RG, RI, RK, RM, SC, SE, SG, SI, SK, SM, TC, TE, TG, TI, TK, TM, UA, UC, UE, UG, UI, UK, VA, VC, VE, VG, VI, VK, WA, WC, WE, WG, WI, WK
Length: 438 amino acids
Theoretical weight: 48.69 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P05214 (Residues: 1-438; Coverage: 97%)
Gene names: Tuba3, Tuba3a, Tuba3b, Tuba7
Sequence domains:
Tektin-2 Chains: B1, B2, B3, B4, B5, B6, B7, B8, B9
Molecule details ›
Chains: B1, B2, B3, B4, B5, B6, B7, B8, B9
Length: 430 amino acids
Theoretical weight: 50.39 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q922G7 (Residues: 1-430; Coverage: 100%)
Gene name: Tekt2
Sequence domains: Tektin family
Nucleoside diphosphate kinase homolog 7 Chains: C, D
Molecule details ›
Chains: C, D
Length: 395 amino acids
Theoretical weight: 44.49 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9QXL8 (Residues: 1-395; Coverage: 100%)
Gene name: Nme7
Sequence domains: Nucleoside diphosphate kinase
Tektin-3 Chains: C1, C2, C3, C4, C5, C6, C7, C8, C9, Ca, Cb, Cc, Cd
Molecule details ›
Chains: C1, C2, C3, C4, C5, C6, C7, C8, C9, Ca, Cb, Cc, Cd
Length: 490 amino acids
Theoretical weight: 56.75 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q6X6Z7 (Residues: 1-490; Coverage: 100%)
Gene name: Tekt3
Sequence domains: Tektin family
Tektin-4 Chains: D1, D2, D3, D4, D5, D6, D7, D8, D9, Da
Molecule details ›
Chains: D1, D2, D3, D4, D5, D6, D7, D8, D9, Da
Length: 447 amino acids
Theoretical weight: 52.12 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q149S1 (Residues: 1-447; Coverage: 100%)
Gene name: Tekt4
Sequence domains: Tektin family
EF-hand domain-containing family member B Chains: E, F
Molecule details ›
Chains: E, F
Length: 853 amino acids
Theoretical weight: 95.89 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8CDU5 (Residues: 1-853; Coverage: 100%)
Gene names: Cfap21, Efhb
Sequence domains: EF-hand domain pair
Tektin bundle-interacting protein 1 Chains: E1, E2, E3, E4
Molecule details ›
Chains: E1, E2, E3, E4
Length: 206 amino acids
Theoretical weight: 23.99 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: A6H6Q4 (Residues: 1-206; Coverage: 100%)
Gene name: Tektip1
Sequence domains: Tektin bundle interacting protein 1
Tektin-5 Chains: F1, F2, F3, F4, F5, F6, F7, F8, F9, Fa, Fb, Fc, Fd, Fe, Ff, Fg, Fh, Fi, Fj, Fk, Fl, Fm
Molecule details ›
Chains: F1, F2, F3, F4, F5, F6, F7, F8, F9, Fa, Fb, Fc, Fd, Fe, Ff, Fg, Fh, Fi, Fj, Fk, Fl, Fm
Length: 557 amino acids
Theoretical weight: 62.82 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: G5E8A8 (Residues: 1-557; Coverage: 100%)
Gene name: Tekt5
Sequence domains: Tektin family
Cilia- and flagella-associated protein 53 Chains: G, H
Molecule details ›
Chains: G, H
Length: 514 amino acids
Theoretical weight: 62.04 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D439 (Residues: 1-514; Coverage: 100%)
Gene names: Ccdc11, Cfap53
Sequence domains: Trichohyalin-plectin-homology domain
EF-hand domain-containing protein 1 Chains: G1, G2, G3
Molecule details ›
Chains: G1, G2, G3
Length: 648 amino acids
Theoretical weight: 75.24 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D9T8 (Residues: 1-648; Coverage: 100%)
Gene name: Efhc1
Sequence domains:
EF-hand domain-containing family member C2 Chains: G4, G5, G6
Molecule details ›
Chains: G4, G5, G6
Length: 750 amino acids
Theoretical weight: 87.76 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D485 (Residues: 1-750; Coverage: 100%)
Gene name: Efhc2
Sequence domains: DM10 domain
Ciliary microtubule inner protein 2A Chains: H1, H2, H3, H4, H5, H6
Molecule details ›
Chains: H1, H2, H3, H4, H5, H6
Length: 319 amino acids
Theoretical weight: 36.66 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D4K5 (Residues: 1-319; Coverage: 100%)
Gene names: Cimip2a, Fam166a
Sequence domains: Protein of unknown function (DUF2475)
Cilia- and flagella-associated protein 95 Chain: I
Molecule details ›
Chain: I
Length: 228 amino acids
Theoretical weight: 26.63 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQC3 (Residues: 1-228; Coverage: 100%)
Gene name: Cfap95
Sequence domains: Protein CFAP95
Ciliary microtubule inner protein 2C Chains: I1, I2, I3
Molecule details ›
Chains: I1, I2, I3
Length: 200 amino acids
Theoretical weight: 23.1 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DAS2 (Residues: 1-200; Coverage: 100%)
Gene names: Cimip2c, Fam166c
Sequence domains: Protein of unknown function (DUF2475)
Cilia- and flagella-associated protein 107 Chain: J
Molecule details ›
Chain: J
Length: 196 amino acids
Theoretical weight: 23.06 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q4KKZ1 (Residues: 1-196; Coverage: 100%)
Gene name: Cfap107
Dual specificity phosphatase 21 Chains: J1, J2, J3
Molecule details ›
Chains: J1, J2, J3
Length: 189 amino acids
Theoretical weight: 21.53 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D9D8 (Residues: 1-189; Coverage: 100%)
Gene name: Dusp21
Sequence domains: Dual specificity phosphatase, catalytic domain
Cilia- and flagella-associated protein 161 Chains: K, L
Molecule details ›
Chains: K, L
Length: 303 amino acids
Theoretical weight: 34.43 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q6P8Y0 (Residues: 1-303; Coverage: 100%)
Gene name: Cfap161
Tektin-like protein 1 Chains: K1, K2, K3, K4, K5
Molecule details ›
Chains: K1, K2, K3, K4, K5
Length: 499 amino acids
Theoretical weight: 57.41 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D4K7 (Residues: 1-499; Coverage: 100%)
Gene names: Ccdc105, Tektl1
Sequence domains: Tektin family
Enkurin Chains: L1, L2, L3, L4
Molecule details ›
Chains: L1, L2, L3, L4
Length: 255 amino acids
Theoretical weight: 29.59 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q6SP97 (Residues: 1-255; Coverage: 100%)
Gene name: Enkur
Sequence domains: Calmodulin-binding
Piercer of microtubule wall 1 protein Chain: M
Molecule details ›
Chain: M
Length: 167 amino acids
Theoretical weight: 18.86 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q5BN45 (Residues: 1-167; Coverage: 100%)
Gene name: Pierce1
Sequence domains: Piercer of microtubule wall 1/2
Sperm-associated microtubule inner protein 10 Chains: M1, M2, M3
Molecule details ›
Chains: M1, M2, M3
Length: 141 amino acids
Theoretical weight: 16.31 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D9I1 (Residues: 1-141; Coverage: 100%)
Gene names: C5orf48, Spmip10, Tex43
Sequence domains: Domain of unknown function (DUF4513)
Piercer of microtubule wall 2 protein Chain: N
Molecule details ›
Chain: N
Length: 122 amino acids
Theoretical weight: 13.73 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: V9GXK1 (Residues: 1-122; Coverage: 100%)
Gene names: Ccpg1os, Pierce2
Sequence domains: Piercer of microtubule wall 1/2
Cilia- and flagella-associated protein 276 Chains: N1, N2, N3, N4
Molecule details ›
Chains: N1, N2, N3, N4
Length: 168 amino acids
Theoretical weight: 18.96 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DAD0 (Residues: 1-168; Coverage: 100%)
Gene name: Cfap276
Sequence domains: Protein of unknown function (DUF3695)
RIB43A-like with coiled-coils protein 2 Chains: O, P, Q, R
Molecule details ›
Chains: O, P, Q, R
Length: 377 amino acids
Theoretical weight: 45.33 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D4Q1 (Residues: 1-377; Coverage: 100%)
Gene name: Ribc2
Sequence domains: RIB43A
Protein Flattop Chains: O1, O2, O3
Molecule details ›
Chains: O1, O2, O3
Length: 189 amino acids
Theoretical weight: 20.58 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q6P8X9 (Residues: 1-189; Coverage: 100%)
Gene names: Cfap126, Fltp
Cilia- and flagella-associated protein 52 Chains: P1, P2, P3
Molecule details ›
Chains: P1, P2, P3
Length: 620 amino acids
Theoretical weight: 68.32 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q5F201 (Residues: 1-620; Coverage: 100%)
Gene names: Cfap52, Wdr16
Sequence domains: WD domain, G-beta repeat
EF-hand calcium-binding domain-containing protein 6 Chains: Q1, Q2, Q3
Molecule details ›
Chains: Q1, Q2, Q3
Length: 1516 amino acids
Theoretical weight: 176.03 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q6P1E8 (Residues: 1-1516; Coverage: 100%)
Gene names: Djbp, Efcab6, Kiaa1672
Sequence domains:
Cilia and flagella associated protein 77 Chains: R1, R2, R3
Molecule details ›
Chains: R1, R2, R3
Length: 283 amino acids
Theoretical weight: 32.79 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: A0A087WRI3 (Residues: 1-283; Coverage: 100%)
Gene names: 1700101E01Rik, Cfap77
Sequence domains: Cilia- and flagella-associated protein 77
Sperm-associated antigen 8 Chains: S, T
Molecule details ›
Chains: S, T
Length: 470 amino acids
Theoretical weight: 50.59 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q3V0Q6 (Residues: 1-470; Coverage: 100%)
Gene name: Spag8
Cilia- and flagella-associated protein 45 Chains: U, V, W, X
Molecule details ›
Chains: U, V, W, X
Length: 551 amino acids
Theoretical weight: 65.96 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D9U9 (Residues: 1-551; Coverage: 100%)
Gene names: Ccdc19, Cfap45, Nesg1
Sequence domains: Trichohyalin-plectin-homology domain
Cilia- and flagella-associated protein 20 Chains: XA, XB, XC, XD, XE, XF, XG
Molecule details ›
Chains: XA, XB, XC, XD, XE, XF, XG
Length: 193 amino acids
Theoretical weight: 22.78 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8BTU1 (Residues: 1-193; Coverage: 100%)
Gene names: Cfap20, Gtl3
Sequence domains: CFA20 domain
Parkin coregulated gene protein homolog Chains: XH, XI, XJ, XK, XL, XM
Molecule details ›
Chains: XH, XI, XJ, XK, XL, XM
Length: 241 amino acids
Theoretical weight: 27.76 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DAK2 (Residues: 1-241; Coverage: 100%)
Gene name: Pacrg
Sequence domains: Parkin co-regulated protein
Cilia- and flagella- associated protein 210 Chains: Y, Z
Molecule details ›
Chains: Y, Z
Length: 547 amino acids
Theoretical weight: 65.27 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: A0JLY1 (Residues: 1-547; Coverage: 100%)
Gene names: Ccdc173, Cfap210
Sequence domains: Trichohyalin-plectin-homology domain
Sperm acrosome-associated protein 9 Chains: YA, YB, YC, YD, YE, YF, YG, YH, YI, YJ, YK, YL, YM, YN, YO, YP, YQ, YR, YS, YT, YU, YV, YW
Molecule details ›
Chains: YA, YB, YC, YD, YE, YF, YG, YH, YI, YJ, YK, YL, YM, YN, YO, YP, YQ, YR, YS, YT, YU, YV, YW
Length: 168 amino acids
Theoretical weight: 19.51 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q7TPM5 (Residues: 1-168; Coverage: 100%)
Gene name: Spaca9
Sequence domains: Sperm acrosome-associated protein 9
Cilia- and flagella-associated protein 141 Chain: a
Molecule details ›
Chain: a
Length: 101 amino acids
Theoretical weight: 12.28 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D9D9 (Residues: 1-101; Coverage: 100%)
Gene name: Cfap141
Sequence domains: Cilia- and flagella-associated protein 141

Ligands and Environments

1 bound ligand:
Ligand GTP 279 x GTP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.5Å
Relevant EMDB volumes: EMD-35230

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