9UBW | pdb_00009ubw

The atomic coordinates of the mouse CatSper dimer

PDB DOI: https://doi.org/10.2210/pdb9UBW/pdb
EM Map EMD-64017: 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the mouse CatSper dimer

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

To be published.

Macromolecule Content

Total Structure Weight: 1,413.31 kDa
Atom Count: 96,544
Modeled Residue Count: 12,042
Deposited Residue Count: 12,130
Unique protein chains: 14

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 1	A, O [auth a]	251	Mus musculus	Mutation(s): 0 Gene Names: Catsper1
UniProt
Find proteins for Q91ZR5 (Mus musculus) Explore Q91ZR5 Go to UniProtKB: Q91ZR5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91ZR5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 2	B, P [auth b]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2ARP9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 3	C, Q [auth c]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q80W99
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 4	D, R [auth d]	250	Mus musculus	Mutation(s): 0 Gene Names: Catsper4
UniProt
Find proteins for Q8BVN3 (Mus musculus) Explore Q8BVN3 Go to UniProtKB: Q8BVN3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8BVN3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit beta	E, S [auth e]	1,065	Mus musculus	Mutation(s): 0 Gene Names: Catsperb
UniProt
Find proteins for A2RTF1 (Mus musculus) Explore A2RTF1 Go to UniProtKB: A2RTF1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2RTF1
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain E Focus chain S [auth e]	Go to GlyGen: A2RTF1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit gamma 2	F, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6KI89
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain F Focus chain T [auth f]	Go to GlyGen: C6KI89-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit delta	G, U [auth g]	733	Mus musculus	Mutation(s): 0 Gene Names: Catsperd, Tmem146
UniProt
Find proteins for E9Q9F6 (Mus musculus) Explore E9Q9F6 Go to UniProtKB: E9Q9F6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E9Q9F6
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain G Focus chain U [auth g]	Go to GlyGen: E9Q9F6-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit epsilon	H, V [auth h]	921	Mus musculus	Mutation(s): 0 Gene Names: Catspere, Catspere1, Gm7068
UniProt
Find proteins for P0DP43 (Mus musculus) Explore P0DP43 Go to UniProtKB: P0DP43
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DP43
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain H Focus chain V [auth h]	Go to GlyGen: P0DP43-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
EF-hand calcium-binding domain-containing protein 9	I, W [auth i]	174	Mus musculus	Mutation(s): 0 Gene Names: Efcab9
UniProt
Find proteins for Q9DAM2 (Mus musculus) Explore Q9DAM2 Go to UniProtKB: Q9DAM2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9DAM2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit TMEM249	J, X [auth j]	168	Mus musculus	Mutation(s): 0 Gene Names: Tmem249
UniProt
Find proteins for A0A2R8VHF7 (Mus musculus) Explore A0A2R8VHF7 Go to UniProtKB: A0A2R8VHF7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2R8VHF7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit zeta	K, Y [auth k]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQP8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier organic anion transporter family member 6C1	L, Z [auth l]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8C0X7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated auxiliary subunit TMEM262	AA [auth m], M	115	Mus musculus	Mutation(s): 0 Gene Names: Tmem262, Catsperh
UniProt
Find proteins for D3Z338 (Mus musculus) Explore D3Z338 Go to UniProtKB: D3Z338
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3Z338
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown protein	BA [auth n], N	28	Mus musculus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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	CA [auth O], MA [auth Y]	7		N-Glycosylation	Interactions Focus chain CA [auth O] Focus chain MA [auth Y] Interactions & Density Focus chain CA [auth O] Focus chain MA [auth Y]

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	DA [auth P], EA [auth Q], GA [auth S], HA [auth T], IA [auth U], DA [auth P], EA [auth Q], GA [auth S], HA [auth T], IA [auth U], NA [auth Z], OA [auth o], QA [auth q], RA [auth r], SA [auth s]	3		N-Glycosylation	Interactions Focus chain DA [auth P] Focus chain EA [auth Q] Focus chain GA [auth S] Focus chain HA [auth T] Focus chain IA [auth U] Focus chain NA [auth Z] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Interactions & Density Focus chain DA [auth P] Focus chain EA [auth Q] Focus chain GA [auth S] Focus chain HA [auth T] Focus chain IA [auth U] Focus chain NA [auth Z] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s]

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	FA [auth R], KA [auth W], PA [auth p], UA [auth u]	2		N-Glycosylation	Interactions Focus chain FA [auth R] Focus chain KA [auth W] Focus chain PA [auth p] Focus chain UA [auth u] Interactions & Density Focus chain FA [auth R] Focus chain KA [auth W] Focus chain PA [auth p] Focus chain UA [auth u]

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	JA [auth V], TA [auth t]	7		N-Glycosylation	Interactions Focus chain JA [auth V] Focus chain TA [auth t] Interactions & Density Focus chain JA [auth V] Focus chain TA [auth t]

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	LA [auth X], VA [auth v]	5		N-Glycosylation	Interactions Focus chain LA [auth X] Focus chain VA [auth v] Interactions & Density Focus chain LA [auth X] Focus chain VA [auth v]

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain PB [auth m] SDF format, chain FB [auth M] MOL2 format, chain PB [auth m] MOL2 format, chain FB [auth M] mmCIF format, chain PB [auth m] mmCIF format, chain FB [auth M]	FB [auth M], PB [auth m]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain FB [auth M] Focus chain PB [auth m] Interactions & Density Focus chain FB [auth M] Focus chain PB [auth m]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain JB [auth e] SDF format, chain ZA [auth E] SDF format, chain YA [auth E] SDF format, chain XA [auth E] SDF format, chain WA [auth E] SDF format, chain OB [auth g] SDF format, chain NB [auth g] SDF format, chain MB [auth f] SDF format, chain LB [auth e] SDF format, chain KB [auth e] SDF format, chain IB [auth e] SDF format, chain HB [auth e] SDF format, chain GB [auth e] SDF format, chain EB [auth G] SDF format, chain DB [auth G] SDF format, chain CB [auth F] SDF format, chain BB [auth E] SDF format, chain AB [auth E] MOL2 format, chain JB [auth e] MOL2 format, chain ZA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain OB [auth g] MOL2 format, chain NB [auth g] MOL2 format, chain MB [auth f] MOL2 format, chain LB [auth e] MOL2 format, chain KB [auth e] MOL2 format, chain IB [auth e] MOL2 format, chain HB [auth e] MOL2 format, chain GB [auth e] MOL2 format, chain EB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain CB [auth F] MOL2 format, chain BB [auth E] MOL2 format, chain AB [auth E] mmCIF format, chain JB [auth e] mmCIF format, chain ZA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain OB [auth g] mmCIF format, chain NB [auth g] mmCIF format, chain MB [auth f] mmCIF format, chain LB [auth e] mmCIF format, chain KB [auth e] mmCIF format, chain IB [auth e] mmCIF format, chain HB [auth e] mmCIF format, chain GB [auth e] mmCIF format, chain EB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain CB [auth F] mmCIF format, chain BB [auth E] mmCIF format, chain AB [auth E]	AB [auth E] BB [auth E] CB [auth F] DB [auth G] EB [auth G] AB [auth E], BB [auth E], CB [auth F], DB [auth G], EB [auth G], GB [auth e], HB [auth e], IB [auth e], JB [auth e], KB [auth e], LB [auth e], MB [auth f], NB [auth g], OB [auth g], WA [auth E], XA [auth E], YA [auth E], ZA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain GB [auth e] Focus chain HB [auth e] Focus chain IB [auth e] Focus chain JB [auth e] Focus chain KB [auth e] Focus chain LB [auth e] Focus chain MB [auth f] Focus chain NB [auth g] Focus chain OB [auth g] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain GB [auth e] Focus chain HB [auth e] Focus chain IB [auth e] Focus chain JB [auth e] Focus chain KB [auth e] Focus chain LB [auth e] Focus chain MB [auth f] Focus chain NB [auth g] Focus chain OB [auth g] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]