9UBX | pdb_00009ubx

The atomic coordinates of the mouse CatSper trimer

• PDB DOI: https://doi.org/10.2210/pdb9UBX/pdb
• EM Map EMD-64028: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Mus musculus
• Expression System: Mus musculus
• Mutation(s): Yes 


• Deposited: 2025-04-03 Released: 2025-12-31 
• Deposition Author(s): Xu, Q., Lin, S., Zhao, Q., Yan, Z., Wu, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Literature

Cryo-EM structure of the mouse CatSper trimer

Xu, Q., Lin, S., Zhao, Q., Yan, Z., Wu, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 42-mer - A3B3C3D3E3F3G3H3I3J3K3L3M3N3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 42-mer - A12B3C3D3E3F3G3H3I3J3K3 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - F2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - E2M2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,119.97 kDa 
• Atom Count: 144,816 
• Modeled Residue Count: 18,063 
• Deposited Residue Count: 18,195 
• Unique protein chains: 14

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 1	A, BA [auth a], O [auth n]	251	Mus musculus	Mutation(s): 0  Gene Names: Catsper1
UniProt
Find proteins for Q91ZR5 (Mus musculus) Explore Q91ZR5  Go to UniProtKB:  Q91ZR5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 2	B, CA [auth b], P [auth o]	281	Mus musculus	Mutation(s): 0  Gene Names: Catsper2
UniProt & NIH Common Fund Data Resources
Find proteins for A2ARP9 (Mus musculus) Explore A2ARP9  Go to UniProtKB:  A2ARP9
IMPC:  MGI:2387404

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 3	C, DA [auth c], Q [auth p]	278	Mus musculus	Mutation(s): 0  Gene Names: Catsper3
UniProt & NIH Common Fund Data Resources
Find proteins for Q80W99 (Mus musculus) Explore Q80W99  Go to UniProtKB:  Q80W99
IMPC:  MGI:1924106

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 4	D, EA [auth d], R [auth q]	250	Mus musculus	Mutation(s): 0  Gene Names: Catsper4
UniProt
Find proteins for Q8BVN3 (Mus musculus) Explore Q8BVN3  Go to UniProtKB:  Q8BVN3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit beta	E, FA [auth e], S [auth r]	1,065	Mus musculus	Mutation(s): 0  Gene Names: Catsperb
UniProt
Find proteins for A2RTF1 (Mus musculus) Explore A2RTF1  Go to UniProtKB:  A2RTF1
Glycosylation
Glycosylation Sites: 7		Go to GlyGen: A2RTF1-1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit gamma 2	F, GA [auth s], T [auth f]	1,042	Mus musculus	Mutation(s): 0  Gene Names: Catsperg2, Catsperg
UniProt
Find proteins for C6KI89 (Mus musculus) Explore C6KI89  Go to UniProtKB:  C6KI89
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: C6KI89-1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit delta	G, HA [auth g], U [auth t]	733	Mus musculus	Mutation(s): 0  Gene Names: Catsperd, Tmem146
UniProt
Find proteins for E9Q9F6 (Mus musculus) Explore E9Q9F6  Go to UniProtKB:  E9Q9F6
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: E9Q9F6-1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit epsilon	H, IA [auth h], V [auth u]	921	Mus musculus	Mutation(s): 0  Gene Names: Catspere, Catspere1, Gm7068
UniProt
Find proteins for P0DP43 (Mus musculus) Explore P0DP43  Go to UniProtKB:  P0DP43
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P0DP43-1

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
EF-hand calcium-binding domain-containing protein 9	I, JA [auth i], PA [auth Q]	174	Mus musculus	Mutation(s): 0  Gene Names: Efcab9
UniProt
Find proteins for Q9DAM2 (Mus musculus) Explore Q9DAM2  Go to UniProtKB:  Q9DAM2

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit TMEM249	J, KA [auth j], W [auth w]	168	Mus musculus	Mutation(s): 0  Gene Names: Tmem249
UniProt
Find proteins for A0A2R8VHF7 (Mus musculus) Explore A0A2R8VHF7  Go to UniProtKB:  A0A2R8VHF7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit zeta	K, LA [auth k], X [auth x]	149	Mus musculus	Mutation(s): 0  Gene Names: Catsperz, Tex40
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQP8 (Mus musculus) Explore Q9CQP8  Go to UniProtKB:  Q9CQP8
IMPC:  MGI:1914327

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier organic anion transporter family member 6C1	L, MA [auth l], Y [auth y]	610	Mus musculus	Mutation(s): 1  Gene Names: Slco6c1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C0X7 (Mus musculus) Explore Q8C0X7  Go to UniProtKB:  Q8C0X7
IMPC:  MGI:1921691

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit TMEM262	M, NA [auth m], Z [auth z]	115	Mus musculus	Mutation(s): 0  Gene Names: Tmem262, Catsperh
UniProt
Find proteins for D3Z338 (Mus musculus) Explore D3Z338  Go to UniProtKB:  D3Z338

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown protein	AA [auth P], N, OA [auth O]	28	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 15
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	AB [auth 0], KB [auth AA], QA [auth R]	7		N-Glycosylation

Entity ID: 16
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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], 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]	3		N-Glycosylation

Entity ID: 17
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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], YA [auth Z]	2		N-Glycosylation

Entity ID: 18
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	HB [auth 7], RB [auth HA], XA [auth Y]	7		N-Glycosylation

Entity ID: 19
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	JB [auth 9], TB [auth JA], ZA [auth v]	5		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR (Subject of Investigation/LOI)	DC [auth M], NC [auth z], XC [auth m]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG (Subject of Investigation/LOI)	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:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Xu, Q., Lin, S., Zhao, Q., Yan, Z., Wu, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release