27CL | pdb_000027cl

Cryo-EM structure of the Vo domain of Concanamycin A-bound V-ATPase from rat brain, state 3-1

PDB DOI: https://doi.org/10.2210/pdb27CL/pdb
EM Map EMD-81057: EMDB EMDataResource

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

Deposited: 2026-05-26 Released: 2026-10-28
Deposition Author(s): Nishida, Y., Akisada, S., 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

Starting Model: experimental
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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 from rat brain, state 3-1

Nishida, Y., Akisada, S., Yokoyama, K.

To be published.

Macromolecule Content

Total Structure Weight: 445.1 kDa
Atom Count: 21,310
Modeled Residue Count: 2,751
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
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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
Entity Groups
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UniProt Group	Q5EB76
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Reference Sequence

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| 3D Structure

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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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
Entity Groups
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UniProt Group	P63081
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Reference Sequence

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| 3D Structure

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 116 kDa subunit a 1	P [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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UniProt Group	P25286
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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 subunit D	Q [auth H]	226	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6P503 (Rattus norvegicus) Explore Q6P503 Go to UniProtKB: Q6P503
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UniProt Group	Q6P503
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1MGD( Subject of Investigation/LOI) Query on A1MGD Download:Ideal Coordinates CCD File SDF format, chain R [auth i] SDF format, chain T [auth j] SDF format, chain U [auth l] SDF format, chain W [auth n] SDF format, chain X [auth n] SDF format, chain Y [auth o] SDF format, chain Z [auth a] SDF format, chain V [auth l] SDF format, chain S [auth i] MOL2 format, chain R [auth i] MOL2 format, chain T [auth j] MOL2 format, chain U [auth l] MOL2 format, chain W [auth n] MOL2 format, chain X [auth n] MOL2 format, chain Y [auth o] MOL2 format, chain Z [auth a] MOL2 format, chain V [auth l] MOL2 format, chain S [auth i] mmCIF format, chain R [auth i] mmCIF format, chain T [auth j] mmCIF format, chain U [auth l] mmCIF format, chain W [auth n] mmCIF format, chain X [auth n] mmCIF format, chain Y [auth o] mmCIF format, chain Z [auth a] mmCIF format, chain V [auth l] mmCIF format, chain S [auth i]	R [auth i] S [auth i] T [auth j] U [auth l] V [auth l] R [auth i], S [auth i], T [auth j], U [auth l], V [auth l], W [auth n], X [auth n], Y [auth o], Z [auth a]	concanamycin A C₄₆ H₇₅ N O₁₄ DJZCTUVALDDONK-CAZRXPRYSA-N		Interactions Focus chain R [auth i] Focus chain S [auth i] Focus chain T [auth j] Focus chain U [auth l] Focus chain V [auth l] Focus chain W [auth n] Focus chain X [auth n] Focus chain Y [auth o] Focus chain Z [auth a] Interactions & Density Focus chain R [auth i] Focus chain S [auth i] Focus chain T [auth j] Focus chain U [auth l] Focus chain V [auth l] Focus chain W [auth n] Focus chain X [auth n] Focus chain Y [auth o] Focus chain Z [auth a]