7EEB

Structure of the CatSpermasome

PDB DOI: https://doi.org/10.2210/pdb7EEB/pdb
EM Map EMD-31076: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Human betaherpesvirus 5, Mus musculus
Expression System: Mus musculus
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2021-03-18 Released: 2021-07-28
Deposition Author(s): Wu, J.P., Ke, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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.

Macromolecule Content

Total Structure Weight: 915.38 kDa
Atom Count: 47,874
Modelled Residue Count: 6,003
Deposited Residue Count: 7,855
Unique protein chains: 14

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enhanced green fluorescent protein,Cation channel sperm-associated protein 1	A	955	Human betaherpesvirus 5, Mus musculus This entity is chimeric	Mutation(s): 0 Gene Names: egfp, Catsper1 Membrane Entity: Yes
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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 2	B	588	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 3	C	395	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein 4	D	442	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein subunit beta	E	1,109	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein subunit gamma 2	F	1,145	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein subunit delta	G	805	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein subunit epsilon	H	985	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Kazal-like domain-containing protein	I [auth L]	706	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein 249	J	171	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein 262	K [auth M]	116	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown	L [auth N]	28	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
EF-hand calcium-binding domain-containing protein 9	M [auth I]	216	Mus musculus	Mutation(s): 0
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
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel sperm-associated protein subunit zeta	N [auth K]	194	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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

Oligosaccharides

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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	O	7		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G01504UZ GlyCosmos: G01504UZ GlyGen: G01504UZ

Entity ID: 16
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], DA [auth d], P, S, T, AA [auth a], DA [auth d], P, S, T, V, X	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Focus chain P Focus chain S Focus chain T Focus chain V Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d] Focus chain P Focus chain S Focus chain T Focus chain V Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 17
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	BA [auth b], Q, R, U, W	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain Q Focus chain R Focus chain U Focus chain W Interactions & Density Focus chain BA [auth b] Focus chain Q Focus chain R Focus chain U Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 18
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], Y	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain Y Interactions & Density Focus chain CA [auth c] Focus chain Y
Glycosylation Resources
GlyTouCan: G89225LT GlyCosmos: G89225LT GlyGen: G89225LT

Entity ID: 19
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[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	Z	7		N/A	Interactions Focus chain Z Interactions & Density Focus chain Z
Glycosylation Resources
GlyTouCan: G42553TN GlyCosmos: G42553TN GlyGen: G42553TN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9Z9 Query on 9Z9 Download Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain HA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain HA [auth A]	FA [auth A], GA [auth A], HA [auth A]	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en C₃₄ H₅₆ O₅ CEEBZAXXSRFQIC-GZSGZGDASA-N		Interactions Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Interactions & Density Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain MA [auth E] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain NA [auth F] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain QA [auth G] SDF format, chain RA [auth H] MOL2 format, chain JA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain QA [auth G] MOL2 format, chain RA [auth H]	JA [auth E] KA [auth E] LA [auth E] MA [auth E] NA [auth F] JA [auth E], KA [auth E], LA [auth E], MA [auth E], NA [auth F], OA [auth G], PA [auth G], QA [auth G], RA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth F] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain RA [auth H] Interactions & Density Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth F] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain RA [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain IA [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain IA [auth D]	EA [auth A], IA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain IA [auth D] Interactions & Density Focus chain EA [auth A] Focus chain IA [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Wu, J.P.

Ke, M.

Revision History (Full details and data files)

Version 1.0: 2021-07-28
Type: Initial release
Version 1.1: 2021-08-11
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

7EEB

Structure of the CatSpermasome

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 15

Glycosylation Resources

Entity ID: 16

Glycosylation Resources

Entity ID: 17

Glycosylation Resources

Entity ID: 18

Glycosylation Resources

Entity ID: 19

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)