36QU | pdb_000036qu

Arabidopsis thaliana V-type ATPase, State 1

PDB DOI: https://doi.org/10.2210/pdb36QU/pdb
EM Map EMD-77786: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Mutation(s): No

Deposited: 2026-06-26 Released: 2026-09-09
Deposition Author(s): Khamina, M., Rubinstein, J.L.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), German Research Foundation (DFG)

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 Arabidopsis thaliana V-type ATPase

Khamina, M., Wunsch, N., Lupanga, U., Fink, F., Wang, H., Schulze, W.X., Schumacher, K., Rubinstein, J.L.

To be published.

Macromolecule Content

Total Structure Weight: 1,005.31 kDa
Atom Count: 54,320
Modeled Residue Count: 8,128
Deposited Residue Count: 9,135
Unique protein chains: 15

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit B1	A [auth F], AA [auth D], DA [auth B]	486	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P11574 (Arabidopsis thaliana) Explore P11574 Go to UniProtKB: P11574
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11574
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit E1	B [auth G], D [auth I], F [auth K]	230	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q39258 (Arabidopsis thaliana) Explore Q39258 Go to UniProtKB: Q39258
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q39258
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit G1	C [auth H], E [auth J], G [auth L]	110	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for O82628 (Arabidopsis thaliana) Explore O82628 Go to UniProtKB: O82628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O82628
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit D	H [auth M]	261	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9XGM1 (Arabidopsis thaliana) Explore Q9XGM1 Go to UniProtKB: Q9XGM1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9XGM1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit F	I [auth N]	128	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9ZQX4 (Arabidopsis thaliana) Explore Q9ZQX4 Go to UniProtKB: Q9ZQX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZQX4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit H	J [auth P]	441	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9LX65 (Arabidopsis thaliana) Explore Q9LX65 Go to UniProtKB: Q9LX65
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LX65
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit AP1 fragment	K [auth b]	321	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q93WB8 (Arabidopsis thaliana) Explore Q93WB8 Go to UniProtKB: Q93WB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93WB8
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c''1	L [auth c]	180	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SZY7 (Arabidopsis thaliana) Explore Q9SZY7 Go to UniProtKB: Q9SZY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SZY7
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit d1	M [auth d]	351	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9LJI5 (Arabidopsis thaliana) Explore Q9LJI5 Go to UniProtKB: Q9LJI5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LJI5
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e2	N [auth e]	70	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SZ13 (Arabidopsis thaliana) Explore Q9SZ13 Go to UniProtKB: Q9SZ13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SZ13
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c1	O [auth g] P [auth h] Q [auth i] R [auth j] S [auth k] O [auth g], P [auth h], Q [auth i], R [auth j], S [auth k], T [auth l], U [auth m], V [auth n], W [auth o]	164	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P0DH92 (Arabidopsis thaliana) Explore P0DH92 Go to UniProtKB: P0DH92
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DH92
Sequence Annotations Expand
Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit AP2 fragment	X [auth r]	364	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9ZSJ7 (Arabidopsis thaliana) Explore Q9ZSJ7 Go to UniProtKB: Q9ZSJ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZSJ7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase catalytic subunit A	EA [auth A], Y [auth C], Z [auth E]	623	Arabidopsis thaliana	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for O23654 (Arabidopsis thaliana) Explore O23654 Go to UniProtKB: O23654
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O23654
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit C	BA [auth O]	375	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SDS7 (Arabidopsis thaliana) Explore Q9SDS7 Go to UniProtKB: Q9SDS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SDS7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit a3	CA [auth a]	821	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q8W4S4 (Arabidopsis thaliana) Explore Q8W4S4 Go to UniProtKB: Q8W4S4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8W4S4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain HA [auth E] MOL2 format, chain HA [auth E] mmCIF format, chain HA [auth E]	HA [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain HA [auth E] Interactions & Density Focus chain HA [auth E]
PLM (Subject of Investigation/LOI) Query on PLM Download:Ideal Coordinates CCD File SDF format, chain GA [auth b] SDF format, chain FA [auth b] MOL2 format, chain GA [auth b] MOL2 format, chain FA [auth b] mmCIF format, chain GA [auth b] mmCIF format, chain FA [auth b]	FA [auth b], GA [auth b]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain FA [auth b] Focus chain GA [auth b] Interactions & Density Focus chain FA [auth b] Focus chain GA [auth b]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain IA [auth E] MOL2 format, chain IA [auth E] mmCIF format, chain IA [auth E]	IA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IA [auth E] Interactions & Density Focus chain IA [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Khamina, M.

Rubinstein, J.L.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT195707
German Research Foundation (DFG)	Germany	CRC1101

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

36QU | pdb_000036qu

Arabidopsis thaliana V-type ATPase, State 1

Literature

Cryo-EM structure of the Arabidopsis thaliana V-type ATPase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Sequence Annotations

Entity ID: 3

UniProt

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Sequence Annotations

Entity ID: 4

UniProt

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Entity ID: 5

UniProt

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Entity ID: 6

UniProt

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Entity ID: 7

UniProt

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Sequence Annotations

Entity ID: 8

UniProt

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Sequence Annotations

Entity ID: 9

UniProt

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Sequence Annotations

Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Sequence Annotations

Entity ID: 12

UniProt

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Sequence Annotations

Entity ID: 13

UniProt

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Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)