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- PDB-9ubx: The atomic coordinates of the mouse CatSper trimer -

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Basic information

Entry
Database: PDB / ID: 9ubx
TitleThe atomic coordinates of the mouse CatSper trimer
Components
  • (Cation channel sperm-associated auxiliary subunit ...) x 7
  • (Cation channel sperm-associated protein ...) x 4
  • EF-hand calcium-binding domain-containing protein 9
  • Solute carrier organic anion transporter family member 6C1
  • Unknown protein
KeywordsPROTEIN TRANSPORT / sperm / hyperactivation / calcium channel
Function / homology
Function and homology information


Sperm Motility And Taxes / CatSper complex / fusion of sperm to egg plasma membrane involved in single fertilization / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / calcium ion sensor activity / male meiotic nuclear division / flagellated sperm motility / organic anion transport / : ...Sperm Motility And Taxes / CatSper complex / fusion of sperm to egg plasma membrane involved in single fertilization / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / calcium ion sensor activity / male meiotic nuclear division / flagellated sperm motility / organic anion transport / : / calcium-activated cation channel activity / fertilization / motile cilium / sodium ion transport / sperm capacitation / regulation of calcium ion transport / monoatomic ion channel complex / sperm flagellum / voltage-gated calcium channel activity / acrosomal vesicle / establishment of localization in cell / calcium ion transport / spermatogenesis / cell differentiation / calmodulin binding / cilium / calcium ion binding / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated auxiliary subunit gamma / Cation channel sperm-associated protein 4 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit delta/epsilon / Cation channel sperm-associated auxiliary subunit TMEM262 / : / : ...Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated auxiliary subunit gamma / Cation channel sperm-associated protein 4 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit delta/epsilon / Cation channel sperm-associated auxiliary subunit TMEM262 / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / CATSPERD, beta-propeller domain / CATSPERG beta-propeller domain / CATSPERB, C-terminal domain / Cation channel sperm-associated auxiliary subunit TMEM249 / CATSPER protein subunit beta protein 1st domain / CATSPER subunit beta protein 2nd domain / CATSPERB head domain / CATSPERB Ig-like domain / CATSPERG N-terminal domain / CATSPERE first N-terminal domain / CATSPERE second N-terminal domain / CATSPERE beta-propeller domain / CATSPERG C-terminal domain / CATSPERE Ig-like domain / CATSPERD/E C-terminal domain / CATSPERG Ig-like domain / CATSPERD Ig-like domain / Cation channel sperm-associated auxiliary subunit zeta / EF-hand calcium-binding domain-containing protein 9 / Organic anion transporter polypeptide / Organic Anion Transporter Polypeptide (OATP) family / Kazal-type serine protease inhibitor domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Voltage-dependent channel domain superfamily / MFS transporter superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
CHOLESTEROL / Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit gamma 2 / Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit delta / Cation channel sperm-associated auxiliary subunit epsilon / Cation channel sperm-associated protein 3 / Cation channel sperm-associated protein 4 ...CHOLESTEROL / Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit gamma 2 / Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit delta / Cation channel sperm-associated auxiliary subunit epsilon / Cation channel sperm-associated protein 3 / Cation channel sperm-associated protein 4 / Solute carrier organic anion transporter family member 6C1 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated auxiliary subunit zeta / EF-hand calcium-binding domain-containing protein 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsXu, Q. / Lin, S. / Zhao, Q. / Yan, Z. / Wu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Molecular basis of the higher-order assembly of CatSper.
Authors: Qikui Xu / Shiyi Lin / Qingqing Zhao / Yanfei Ru / Hang Kang / Xuhui Zeng / Min Jiang / Zhen Yan / Jianping Wu /
Abstract: CatSper serves as the primary Ca 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 ...CatSper serves as the primary Ca 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.
History
DepositionApr 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cation channel sperm-associated protein 1
B: Cation channel sperm-associated protein 2
C: Cation channel sperm-associated protein 3
D: Cation channel sperm-associated protein 4
E: Cation channel sperm-associated auxiliary subunit beta
F: Cation channel sperm-associated auxiliary subunit gamma 2
G: Cation channel sperm-associated auxiliary subunit delta
H: Cation channel sperm-associated auxiliary subunit epsilon
I: EF-hand calcium-binding domain-containing protein 9
J: Cation channel sperm-associated auxiliary subunit TMEM249
K: Cation channel sperm-associated auxiliary subunit zeta
L: Solute carrier organic anion transporter family member 6C1
M: Cation channel sperm-associated auxiliary subunit TMEM262
N: Unknown protein
n: Cation channel sperm-associated protein 1
o: Cation channel sperm-associated protein 2
p: Cation channel sperm-associated protein 3
q: Cation channel sperm-associated protein 4
r: Cation channel sperm-associated auxiliary subunit beta
f: Cation channel sperm-associated auxiliary subunit gamma 2
t: Cation channel sperm-associated auxiliary subunit delta
u: Cation channel sperm-associated auxiliary subunit epsilon
w: Cation channel sperm-associated auxiliary subunit TMEM249
x: Cation channel sperm-associated auxiliary subunit zeta
y: Solute carrier organic anion transporter family member 6C1
z: Cation channel sperm-associated auxiliary subunit TMEM262
P: Unknown protein
a: Cation channel sperm-associated protein 1
b: Cation channel sperm-associated protein 2
c: Cation channel sperm-associated protein 3
d: Cation channel sperm-associated protein 4
e: Cation channel sperm-associated auxiliary subunit beta
s: Cation channel sperm-associated auxiliary subunit gamma 2
g: Cation channel sperm-associated auxiliary subunit delta
h: Cation channel sperm-associated auxiliary subunit epsilon
i: EF-hand calcium-binding domain-containing protein 9
j: Cation channel sperm-associated auxiliary subunit TMEM249
k: Cation channel sperm-associated auxiliary subunit zeta
l: Solute carrier organic anion transporter family member 6C1
m: Cation channel sperm-associated auxiliary subunit TMEM262
O: Unknown protein
Q: EF-hand calcium-binding domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,119,967102
Polymers2,091,34742
Non-polymers28,62060
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Cation channel sperm-associated protein ... , 4 types, 12 molecules AnaBobCpcDqd

#1: Protein Cation channel sperm-associated protein 1 / CatSper1


Mass: 29080.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper1 / Production host: Mus musculus (house mouse) / References: UniProt: Q91ZR5
#2: Protein Cation channel sperm-associated protein 2 / CatSper2


Mass: 33115.477 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper2 / Production host: Mus musculus (house mouse) / References: UniProt: A2ARP9
#3: Protein Cation channel sperm-associated protein 3 / CatSper3


Mass: 32308.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper3 / Production host: Mus musculus (house mouse) / References: UniProt: Q80W99
#4: Protein Cation channel sperm-associated protein 4 / CatSper4


Mass: 28880.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper4 / Production host: Mus musculus (house mouse) / References: UniProt: Q8BVN3

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Cation channel sperm-associated auxiliary subunit ... , 7 types, 21 molecules EreFfsGtgHuhJwjKxkMzm

#5: Protein Cation channel sperm-associated auxiliary subunit beta / CatSper-beta


Mass: 121580.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperb / Production host: Mus musculus (house mouse) / References: UniProt: A2RTF1
#6: Protein Cation channel sperm-associated auxiliary subunit gamma 2


Mass: 119864.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperg2, Catsperg / Production host: Mus musculus (house mouse) / References: UniProt: C6KI89
#7: Protein Cation channel sperm-associated auxiliary subunit delta / CatSper-delta / CatSperdelta / Transmembrane protein 146


Mass: 82834.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperd, Tmem146 / Production host: Mus musculus (house mouse) / References: UniProt: E9Q9F6
#8: Protein Cation channel sperm-associated auxiliary subunit epsilon / CatSper-epsilon / CatSperepsilon / C1orf101-like protein


Mass: 107004.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catspere, Catspere1, Gm7068 / Production host: Mus musculus (house mouse) / References: UniProt: P0DP43
#10: Protein Cation channel sperm-associated auxiliary subunit TMEM249 / Transmembrane protein 249


Mass: 19898.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmem249 / Production host: Mus musculus (house mouse) / References: UniProt: A0A2R8VHF7
#11: Protein Cation channel sperm-associated auxiliary subunit zeta / CatSper-zeta / CatSperzeta / Protein expressed in male leptotene and zygotene spermatocytes 622 / ...CatSper-zeta / CatSperzeta / Protein expressed in male leptotene and zygotene spermatocytes 622 / MLZ-622 / Testis-expressed protein 40


Mass: 17504.592 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperz, Tex40 / Production host: Mus musculus (house mouse) / References: UniProt: Q9CQP8
#13: Protein Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit eta / Transmembrane protein 262


Mass: 13350.882 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmem262, Catsperh / Production host: Mus musculus (house mouse) / References: UniProt: D3Z338

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Protein , 2 types, 6 molecules IiQLyl

#9: Protein EF-hand calcium-binding domain-containing protein 9


Mass: 20942.268 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Efcab9 / Production host: Mus musculus (house mouse) / References: UniProt: Q9DAM2
#12: Protein Solute carrier organic anion transporter family member 6C1


Mass: 68349.680 Da / Num. of mol.: 3 / Mutation: A224G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slco6c1 / Production host: Mus musculus (house mouse) / References: UniProt: Q8C0X7

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Protein/peptide / Non-polymers , 2 types, 6 molecules NPO

#14: Protein/peptide Unknown protein


Mass: 2400.951 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#21: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 6 types, 57 molecules

#15: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-beta-D- ...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-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpb1-3[DManpb1-3DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#16: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#17: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#18: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[beta-D- ...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-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#19: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#20: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotrimer of the mouse CatSper / Type: COMPLEX / Entity ID: #1-#14 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69708 / Symmetry type: POINT

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