8I7R | pdb_00008i7r

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

In-cell structural insight into the stability of sperm microtubule doublet.

Tai, L.Yin, G.Huang, X.Sun, F.Zhu, Y.

(2023) Cell Discov 9: 116-116

  • DOI: https://doi.org/10.1038/s41421-023-00606-3
  • Primary Citation of Related Structures:  
    8I7O, 8I7R

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis-specific nuclear structural protein 1A,
R [auth B]
491Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-1B [auth A1],
C [auth A2],
D [auth A3],
E [auth A4]
418Mus musculusMutation(s): 0 
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IMPC:  MGI:1333819
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-4B chain427Mus musculusMutation(s): 0 
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IMPC:  MGI:1915472
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Detyrosinated tubulin alpha-3 chain438Mus musculusMutation(s): 0 
EC: 3.6.5
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-2430Mus musculusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase 7NA [auth C],
NB [auth D]
395Mus musculusMutation(s): 0 
EC: 2.7.4.6 (PDB Primary Data), 3.1 (UniProt), 2.7 (UniProt)
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IMPC:  MGI:2449121
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-3490Mus musculusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-4447Mus musculusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing family member BBD [auth F],
KC [auth E]
853Mus musculusMutation(s): 0 
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IMPC:  MGI:3045296
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin bundle-interacting protein 1LC [auth E1],
MC [auth E2],
NC [auth E3],
OC [auth E4]
206Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-5557Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 53DF [auth H],
KE [auth G]
514Mus musculusMutation(s): 0 
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IMPC:  MGI:1921703
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing protein 1LE [auth G1],
ME [auth G2],
NE [auth G3]
648Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing family member C2OE [auth G4],
PE [auth G5],
QE [auth G6]
750Mus musculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM166A319Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 95WF [auth I]228Mus musculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM166CXF [auth I1],
YF [auth I2],
ZF [auth I3]
200Mus musculusMutation(s): 0 
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IMPC:  MGI:1922684
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 107NG [auth J]196Mus musculusMutation(s): 0 
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IMPC:  MGI:1916614
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity phosphatase 21OG [auth J1],
PG [auth J2],
QG [auth J3]
189Mus musculusMutation(s): 0 
EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 161DH [auth K],
VH [auth L]
303Mus musculusMutation(s): 0 
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IMPC:  MGI:1922806
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 105EH [auth K1],
FH [auth K2],
GH [auth K3],
HH [auth K4],
IH [auth K5]
499Mus musculusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
EnkurinWH [auth L1],
XH [auth L2],
YH [auth L3],
ZH [auth L4]
255Mus musculusMutation(s): 0 
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IMPC:  MGI:1918483
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Piercer of microtubule wall 1 proteinMI [auth M]167Mus musculusMutation(s): 0 
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IMPC:  MGI:1916577
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Testis-expressed protein 43NI [auth M1],
OI [auth M2],
PI [auth M3]
141Mus musculusMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Piercer of microtubule wall 2 proteinCJ [auth N]122Mus musculusMutation(s): 0 
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IMPC:  MGI:3648770
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 276DJ [auth N1],
EJ [auth N2],
FJ [auth N3],
GJ [auth N4]
168Mus musculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43A-like with coiled-coils protein 2AL [auth Q],
JK [auth P],
QL [auth R],
TJ [auth O]
377Mus musculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FlattopUJ [auth O1],
VJ [auth O2],
WJ [auth O3]
189Mus musculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 52KK [auth P1],
LK [auth P2],
MK [auth P3]
620Mus musculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand calcium-binding domain-containing protein 6BL [auth Q1],
CL [auth Q2],
DL [auth Q3]
1,516Mus musculusMutation(s): 0 
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IMPC:  MGI:1924877
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella-associated protein 77RL [auth R1],
SL [auth R2],
TL [auth R3]
283Mus musculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm-associated antigen 8GM [auth S],
TM [auth T]
470Mus musculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 45HN [auth U],
HO [auth W],
UN [auth V],
UO [auth X]
551Mus musculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 20193Mus musculusMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Parkin coregulated gene protein homolog241Mus musculusMutation(s): 0 
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IMPC:  MGI:1916560
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 210GQ [auth Z],
IP [auth Y]
547Mus musculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm acrosome-associated protein 9168Mus musculusMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 141HQ [auth a]101Mus musculusMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AAA [auth UJ]
ABA [auth WL]
AR [auth BH]
AS [auth DI]
AT [auth FK]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31925026

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references