25YS | pdb_000025ys

Cryo-EM structure of the Vo domain of Concanamycin A-bound V-ATPase on rat synaptic vesicles, state 3

PDB DOI: https://doi.org/10.2210/pdb25YS/pdb
EM Map EMD-80481: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Rattus norvegicus
Mutation(s): No

Deposited: 2026-04-23 Released: 2026-10-28
Deposition Author(s): Nishida, Y., Yokoyama, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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 Vo domain of Concanamycin A-bound V-ATPase on rat synaptic vesicles, state 3

Nishida, Y., Yokoyama, K.

To be published.

Macromolecule Content

Total Structure Weight: 469.01 kDa
Atom Count: 23,318
Modeled Residue Count: 2,794
Deposited Residue Count: 4,007
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit S1	A [auth P]	463	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for O54715 (Rattus norvegicus) Explore O54715 Go to UniProtKB: O54715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O54715
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 21 kDa proteolipid subunit c''	B [auth b]	205	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for B0K022 (Rattus norvegicus) Explore B0K022 Go to UniProtKB: B0K022
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0K022
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit	C [auth d]	351	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5M7T6 (Rattus norvegicus) Explore Q5M7T6 Go to UniProtKB: Q5M7T6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M7T6
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e 2	D [auth e]	81	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5EB76 (Rattus norvegicus) Explore Q5EB76 Go to UniProtKB: Q5EB76
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5EB76
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease K	E [auth f]	98	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for D3ZIM6 (Rattus norvegicus) Explore D3ZIM6 Go to UniProtKB: D3ZIM6
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3ZIM6
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 16 kDa proteolipid subunit c	F [auth h] G [auth i] H [auth j] I [auth k] J [auth l] F [auth h], G [auth i], H [auth j], I [auth k], J [auth l], K [auth m], L [auth n], M [auth o], O [auth r]	155	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P63081 (Rattus norvegicus) Explore P63081 Go to UniProtKB: P63081
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63081
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin receptor	N [auth p]	350	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6AXS4 (Rattus norvegicus) Explore Q6AXS4 Go to UniProtKB: Q6AXS4
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UniProt Group	Q6AXS4
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit D	P [auth H]	226	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6P503 (Rattus norvegicus) Explore Q6P503 Go to UniProtKB: Q6P503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P503
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a 1	Q [auth a]	838	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P25286 (Rattus norvegicus) Explore P25286 Go to UniProtKB: P25286
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25286
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Reference Sequence

Oligosaccharides

Help

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-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	R [auth Z]	9		N/A	Interactions Focus chain R [auth Z] Interactions & Density Focus chain R [auth Z]

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1MGD Query on A1MGD Download:Ideal Coordinates CCD File SDF format, chain TA [auth l] SDF format, chain SA [auth l] SDF format, chain OB [auth a] SDF format, chain NA [auth k] SDF format, chain DB [auth n] SDF format, chain DA [auth i] SDF format, chain CB [auth n] SDF format, chain AA [auth h] MOL2 format, chain TA [auth l] MOL2 format, chain SA [auth l] MOL2 format, chain OB [auth a] MOL2 format, chain NA [auth k] MOL2 format, chain DB [auth n] MOL2 format, chain DA [auth i] MOL2 format, chain CB [auth n] MOL2 format, chain AA [auth h] mmCIF format, chain TA [auth l] mmCIF format, chain SA [auth l] mmCIF format, chain OB [auth a] mmCIF format, chain NA [auth k] mmCIF format, chain DB [auth n] mmCIF format, chain DA [auth i] mmCIF format, chain CB [auth n] mmCIF format, chain AA [auth h]	AA [auth h] CB [auth n] DA [auth i] DB [auth n] NA [auth k] AA [auth h], CB [auth n], DA [auth i], DB [auth n], NA [auth k], OB [auth a], SA [auth l], TA [auth l]	concanamycin A C₄₆ H₇₅ N O₁₄ DJZCTUVALDDONK-CAZRXPRYSA-N		Interactions Focus chain AA [auth h] Focus chain CB [auth n] Focus chain DA [auth i] Focus chain DB [auth n] Focus chain NA [auth k] Focus chain OB [auth a] Focus chain SA [auth l] Focus chain TA [auth l] Interactions & Density Focus chain AA [auth h] Focus chain CB [auth n] Focus chain DA [auth i] Focus chain DB [auth n] Focus chain NA [auth k] Focus chain OB [auth a] Focus chain SA [auth l] Focus chain TA [auth l]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain U [auth b] SDF format, chain T [auth b] SDF format, chain S [auth P] SDF format, chain RB [auth a] SDF format, chain RA [auth k] MOL2 format, chain U [auth b] MOL2 format, chain T [auth b] MOL2 format, chain S [auth P] MOL2 format, chain RB [auth a] MOL2 format, chain RA [auth k] mmCIF format, chain U [auth b] mmCIF format, chain T [auth b] mmCIF format, chain S [auth P] mmCIF format, chain RB [auth a] mmCIF format, chain RA [auth k]	RA [auth k], RB [auth a], S [auth P], T [auth b], U [auth b]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain RA [auth k] Focus chain RB [auth a] Focus chain S [auth P] Focus chain T [auth b] Focus chain U [auth b] Interactions & Density Focus chain RA [auth k] Focus chain RB [auth a] Focus chain S [auth P] Focus chain T [auth b] Focus chain U [auth b]
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain Z [auth e] SDF format, chain Y [auth b] SDF format, chain W [auth b] SDF format, chain V [auth b] SDF format, chain TB [auth a] SDF format, chain SB [auth a] SDF format, chain NB [auth p] SDF format, chain MB [auth p] SDF format, chain IA [auth j] MOL2 format, chain Z [auth e] MOL2 format, chain Y [auth b] MOL2 format, chain W [auth b] MOL2 format, chain V [auth b] MOL2 format, chain TB [auth a] MOL2 format, chain SB [auth a] MOL2 format, chain NB [auth p] MOL2 format, chain MB [auth p] MOL2 format, chain IA [auth j] mmCIF format, chain Z [auth e] mmCIF format, chain Y [auth b] mmCIF format, chain W [auth b] mmCIF format, chain V [auth b] mmCIF format, chain TB [auth a] mmCIF format, chain SB [auth a] mmCIF format, chain NB [auth p] mmCIF format, chain MB [auth p] mmCIF format, chain IA [auth j]	IA [auth j] MB [auth p] NB [auth p] SB [auth a] TB [auth a] IA [auth j], MB [auth p], NB [auth p], SB [auth a], TB [auth a], V [auth b], W [auth b], Y [auth b], Z [auth e]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain IA [auth j] Focus chain MB [auth p] Focus chain NB [auth p] Focus chain SB [auth a] Focus chain TB [auth a] Focus chain V [auth b] Focus chain W [auth b] Focus chain Y [auth b] Focus chain Z [auth e] Interactions & Density Focus chain IA [auth j] Focus chain MB [auth p] Focus chain NB [auth p] Focus chain SB [auth a] Focus chain TB [auth a] Focus chain V [auth b] Focus chain W [auth b] Focus chain Y [auth b] Focus chain Z [auth e]
WJP Query on WJP Download:Ideal Coordinates CCD File SDF format, chain PB [auth a] MOL2 format, chain PB [auth a] mmCIF format, chain PB [auth a]	PB [auth a]	methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate C₂₆ H₄₈ O₇ P₂ GDOCHZBDTMOKKR-FEJNUDJDSA-N		Interactions Focus chain PB [auth a] Interactions & Density Focus chain PB [auth a]
LP3 Query on LP3 Download:Ideal Coordinates CCD File SDF format, chain QB [auth a] MOL2 format, chain QB [auth a] mmCIF format, chain QB [auth a]	QB [auth a]	(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE C₂₆ H₅₅ N O₇ P IHNKQIMGVNPMTC-RUZDIDTESA-O		Interactions Focus chain QB [auth a] Interactions & Density Focus chain QB [auth a]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain ZA [auth m] SDF format, chain YA [auth m] SDF format, chain XA [auth l] SDF format, chain X [auth b] SDF format, chain WA [auth l] SDF format, chain VA [auth l] SDF format, chain UA [auth l] SDF format, chain QA [auth k] SDF format, chain PA [auth k] SDF format, chain OA [auth k] SDF format, chain MA [auth j] SDF format, chain LB [auth o] SDF format, chain LA [auth j] SDF format, chain KB [auth o] SDF format, chain KA [auth j] SDF format, chain JB [auth o] SDF format, chain JA [auth j] SDF format, chain IB [auth o] SDF format, chain HB [auth n] SDF format, chain HA [auth i] SDF format, chain GB [auth n] SDF format, chain GA [auth i] SDF format, chain FB [auth n] SDF format, chain FA [auth i] SDF format, chain EB [auth n] SDF format, chain EA [auth i] SDF format, chain CA [auth h] SDF format, chain BB [auth m] SDF format, chain BA [auth h] SDF format, chain AB [auth m] MOL2 format, chain ZA [auth m] MOL2 format, chain YA [auth m] MOL2 format, chain XA [auth l] MOL2 format, chain X [auth b] MOL2 format, chain WA [auth l] MOL2 format, chain VA [auth l] MOL2 format, chain UA [auth l] MOL2 format, chain QA [auth k] MOL2 format, chain PA [auth k] MOL2 format, chain OA [auth k] MOL2 format, chain MA [auth j] MOL2 format, chain LB [auth o] MOL2 format, chain LA [auth j] MOL2 format, chain KB [auth o] MOL2 format, chain KA [auth j] MOL2 format, chain JB [auth o] MOL2 format, chain JA [auth j] MOL2 format, chain IB [auth o] MOL2 format, chain HB [auth n] MOL2 format, chain HA [auth i] MOL2 format, chain GB [auth n] MOL2 format, chain GA [auth i] MOL2 format, chain FB [auth n] MOL2 format, chain FA [auth i] MOL2 format, chain EB [auth n] MOL2 format, chain EA [auth i] MOL2 format, chain CA [auth h] MOL2 format, chain BB [auth m] MOL2 format, chain BA [auth h] MOL2 format, chain AB [auth m] mmCIF format, chain ZA [auth m] mmCIF format, chain YA [auth m] mmCIF format, chain XA [auth l] mmCIF format, chain X [auth b] mmCIF format, chain WA [auth l] mmCIF format, chain VA [auth l] mmCIF format, chain UA [auth l] mmCIF format, chain QA [auth k] mmCIF format, chain PA [auth k] mmCIF format, chain OA [auth k] mmCIF format, chain MA [auth j] mmCIF format, chain LB [auth o] mmCIF format, chain LA [auth j] mmCIF format, chain KB [auth o] mmCIF format, chain KA [auth j] mmCIF format, chain JB [auth o] mmCIF format, chain JA [auth j] mmCIF format, chain IB [auth o] mmCIF format, chain HB [auth n] mmCIF format, chain HA [auth i] mmCIF format, chain GB [auth n] mmCIF format, chain GA [auth i] mmCIF format, chain FB [auth n] mmCIF format, chain FA [auth i] mmCIF format, chain EB [auth n] mmCIF format, chain EA [auth i] mmCIF format, chain CA [auth h] mmCIF format, chain BB [auth m] mmCIF format, chain BA [auth h] mmCIF format, chain AB [auth m]	AB [auth m] BA [auth h] BB [auth m] CA [auth h] EA [auth i] AB [auth m], BA [auth h], BB [auth m], CA [auth h], EA [auth i], EB [auth n], FA [auth i], FB [auth n], GA [auth i], GB [auth n], HA [auth i], HB [auth n], IB [auth o], JA [auth j], JB [auth o], KA [auth j], KB [auth o], LA [auth j], LB [auth o], MA [auth j], OA [auth k], PA [auth k], QA [auth k], UA [auth l], VA [auth l], WA [auth l], X [auth b], XA [auth l], YA [auth m], ZA [auth m]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain AB [auth m] Focus chain BA [auth h] Focus chain BB [auth m] Focus chain CA [auth h] Focus chain EA [auth i] Focus chain EB [auth n] Focus chain FA [auth i] Focus chain FB [auth n] Focus chain GA [auth i] Focus chain GB [auth n] Focus chain HA [auth i] Focus chain HB [auth n] Focus chain IB [auth o] Focus chain JA [auth j] Focus chain JB [auth o] Focus chain KA [auth j] Focus chain KB [auth o] Focus chain LA [auth j] Focus chain LB [auth o] Focus chain MA [auth j] Focus chain OA [auth k] Focus chain PA [auth k] Focus chain QA [auth k] Focus chain UA [auth l] Focus chain VA [auth l] Focus chain WA [auth l] Focus chain X [auth b] Focus chain XA [auth l] Focus chain YA [auth m] Focus chain ZA [auth m] Interactions & Density Focus chain AB [auth m] Focus chain BA [auth h] Focus chain BB [auth m] Focus chain CA [auth h] Focus chain EA [auth i] Focus chain EB [auth n] Focus chain FA [auth i] Focus chain FB [auth n] Focus chain GA [auth i] Focus chain GB [auth n] Focus chain HA [auth i] Focus chain HB [auth n] Focus chain IB [auth o] Focus chain JA [auth j] Focus chain JB [auth o] Focus chain KA [auth j] Focus chain KB [auth o] Focus chain LA [auth j] Focus chain LB [auth o] Focus chain MA [auth j] Focus chain OA [auth k] Focus chain PA [auth k] Focus chain QA [auth k] Focus chain UA [auth l] Focus chain VA [auth l] Focus chain WA [auth l] Focus chain X [auth b] Focus chain XA [auth l] Focus chain YA [auth m] Focus chain ZA [auth m]