9UBX | pdb_00009ubx

The atomic coordinates of the mouse CatSper trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of the higher-order assembly of CatSper.

Xu, Q.Lin, S.Zhao, Q.Ru, Y.Kang, H.Zeng, X.Jiang, M.Yan, Z.Wu, J.

(2026) Proc Natl Acad Sci U S A 123: e2510754123-e2510754123

  • DOI: https://doi.org/10.1073/pnas.2510754123
  • Primary Citation of Related Structures:  
    9UBW, 9UBX

  • PubMed Abstract: 

    CatSper serves as the primary Ca 2+ entry pathway in the principal piece of sperm flagellum and is crucial for sperm motility and fertility. Sperm lacking functional CatSper channels fail to undergo hyperactivation during fertilization, leading to complete male infertility. Along the longitudinal axis of the sperm flagellum, staggered CatSper complexes align in a hand-in-hand arrangement, forming a distinctive quadrilinear zigzag arrays known as CatSper nanodomains. However, the molecular details of how CatSper oligomerizes to form such higher-order assembly remain unclear. In this study, we present the cryoelectron microscopy (cryo-EM) structures of native CatSper dimer (~1.5 MDa) and trimer (~2.3 MDa) megacomplexes, which represent the fundamental units of the zigzag array. We reveal the overall configuration of the zigzag assembly by characterizing the two distinct dimer interfaces that mediate CatSper oligomerization. Specifically, we elucidate the interaction details of two extracellular interfaces formed by CATSPERβ and CATSPERγ at the two dimer interfaces, respectively, and find that CATSPERη, a recently identified component of CatSper, constitutes the transmembrane interface within one of these dimer interfaces. Functional studies in mice demonstrate that CATSPERη is essential for the formation of functional CatSper on the sperm flagellum, and CATSPERη-deficient sperm fail to hyperactivate during fertilization, resulting in male infertility both in vivo and in vitro. Our data provide insights into the higher-order assembly of CatSper at the molecular level, offering clues for the development of male contraceptives.


  • Organizational Affiliation
    • State Key Laboratory of Gene Expression, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated protein 1A,
BA [auth a],
O [auth n]
251Mus musculusMutation(s): 0 
Gene Names: Catsper1
UniProt
Find proteins for Q91ZR5 (Mus musculus)
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UniProt GroupQ91ZR5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated protein 2B,
CA [auth b],
P [auth o]
281Mus musculusMutation(s): 0 
Gene Names: Catsper2
UniProt & NIH Common Fund Data Resources
Find proteins for A2ARP9 (Mus musculus)
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IMPC:  MGI:2387404
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UniProt GroupA2ARP9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated protein 3C,
DA [auth c],
Q [auth p]
278Mus musculusMutation(s): 0 
Gene Names: Catsper3
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:1924106
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UniProt GroupQ80W99
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated protein 4D,
EA [auth d],
R [auth q]
250Mus musculusMutation(s): 0 
Gene Names: Catsper4
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated auxiliary subunit betaE,
FA [auth e],
S [auth r]
1,065Mus musculusMutation(s): 0 
Gene Names: Catsperb
UniProt
Find proteins for A2RTF1 (Mus musculus)
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UniProt GroupA2RTF1
Glycosylation
Glycosylation Sites: 7Go to GlyGen: A2RTF1-1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated auxiliary subunit gamma 2F,
GA [auth s],
T [auth f]
1,042Mus musculusMutation(s): 0 
Gene Names: Catsperg2Catsperg
UniProt
Find proteins for C6KI89 (Mus musculus)
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Glycosylation
Glycosylation Sites: 3Go to GlyGen: C6KI89-1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated auxiliary subunit deltaG,
HA [auth g],
U [auth t]
733Mus musculusMutation(s): 0 
Gene Names: CatsperdTmem146
UniProt
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Glycosylation
Glycosylation Sites: 4Go to GlyGen: E9Q9F6-1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated auxiliary subunit epsilonH,
IA [auth h],
V [auth u]
921Mus musculusMutation(s): 0 
Gene Names: CatspereCatspere1Gm7068
UniProt
Find proteins for P0DP43 (Mus musculus)
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Glycosylation
Glycosylation Sites: 5Go to GlyGen: P0DP43-1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand calcium-binding domain-containing protein 9I,
JA [auth i],
PA [auth Q]
174Mus musculusMutation(s): 0 
Gene Names: Efcab9
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated auxiliary subunit TMEM249J,
KA [auth j],
W [auth w]
168Mus musculusMutation(s): 0 
Gene Names: Tmem249
UniProt
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UniProt GroupA0A2R8VHF7
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated auxiliary subunit zetaK,
LA [auth k],
X [auth x]
149Mus musculusMutation(s): 0 
Gene Names: CatsperzTex40
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IMPC:  MGI:1914327
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier organic anion transporter family member 6C1L,
MA [auth l],
Y [auth y]
610Mus musculusMutation(s): 1 
Gene Names: Slco6c1
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IMPC:  MGI:1921691
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cation channel sperm-associated auxiliary subunit TMEM262M,
NA [auth m],
Z [auth z]
115Mus musculusMutation(s): 0 
Gene Names: Tmem262Catsperh
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown proteinAA [auth P],
N,
OA [auth O]
28Mus musculusMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 15
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAB [auth 0],
KB [auth AA],
QA [auth R]
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G01504UZ
GlyCosmos:  G01504UZ
GlyGen:  G01504UZ
Entity ID: 16
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BB [auth 1],
CB [auth 2],
EB [auth 4],
FB [auth 5],
GB [auth 6],
BB [auth 1],
CB [auth 2],
EB [auth 4],
FB [auth 5],
GB [auth 6],
LB [auth BA],
MB [auth CA],
OB [auth EA],
PB [auth FA],
QB [auth GA],
RA [auth S],
SA [auth T],
UA [auth V],
VA [auth W],
WA [auth X]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 17
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DB [auth 3],
IB [auth 8],
NB [auth DA],
SB [auth IA],
TA [auth U],
DB [auth 3],
IB [auth 8],
NB [auth DA],
SB [auth IA],
TA [auth U],
YA [auth Z]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 18
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseHB [auth 7],
RB [auth HA],
XA [auth Y]
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42553TN
GlyCosmos:  G42553TN
GlyGen:  G42553TN
Entity ID: 19
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJB [auth 9],
TB [auth JA],
ZA [auth v]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G89225LT
GlyCosmos:  G89225LT
GlyGen:  G89225LT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
DC [auth M],
NC [auth z],
XC [auth m]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AC [auth F]
BC [auth G]
CC [auth G]
EC [auth r]
FC [auth r]
AC [auth F],
BC [auth G],
CC [auth G],
EC [auth r],
FC [auth r],
GC [auth r],
HC [auth r],
IC [auth r],
JC [auth r],
KC [auth f],
LC [auth t],
MC [auth t],
OC [auth e],
PC [auth e],
QC [auth e],
RC [auth e],
SC [auth e],
TC [auth e],
UB [auth E],
UC [auth s],
VB [auth E],
VC [auth g],
WB [auth E],
WC [auth g],
XB [auth E],
YB [auth E],
ZB [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references