7UZF | pdb_00007uzf

Rat Kidney V-ATPase with SidK, State 1

PDB DOI: https://doi.org/10.2210/pdb7UZF/pdb
EM Map EMD-26909: EMDB EMDataResource

Classification: PROTON TRANSPORT
Organism(s): Rattus norvegicus, Legionella pneumophila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-09 Released: 2023-11-22
Deposition Author(s): Rubinstein, J.L., Abbas, Y.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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

Structure of V-ATPase with NCOA7B

Abbas, Y.M., Rubinstein, J.L.

To be published.

Macromolecule Content

Total Structure Weight: 1,144.29 kDa
Atom Count: 71,930
Modeled Residue Count: 9,170
Deposited Residue Count: 10,268
Unique protein chains: 17

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase H+-transporting V1 subunit A	A, B, C	617	Rattus norvegicus	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for D4A133 (Rattus norvegicus) Explore D4A133 Go to UniProtKB: D4A133
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D4A133
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit B, brain isoform	D, E, F	511	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P62815 (Rattus norvegicus) Explore P62815 Go to UniProtKB: P62815
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62815
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit C 1	G	382	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5FVI6 (Rattus norvegicus) Explore Q5FVI6 Go to UniProtKB: Q5FVI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5FVI6
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase H+-transporting V1 subunit D	H	247	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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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit E 1	I, J, K	226	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6PCU2 (Rattus norvegicus) Explore Q6PCU2 Go to UniProtKB: Q6PCU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6PCU2
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit F	L	119	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P50408 (Rattus norvegicus) Explore P50408 Go to UniProtKB: P50408
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50408
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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 G	M, N, O	118	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for B2GUV5 (Rattus norvegicus) Explore B2GUV5 Go to UniProtKB: B2GUV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2GUV5
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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 H	P	483	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for A0A0G2K9J2 (Rattus norvegicus) Explore A0A0G2K9J2 Go to UniProtKB: A0A0G2K9J2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0G2K9J2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Effector SidK	Q, R, S	280	Legionella pneumophila	Mutation(s): 0 Gene Names: lpg0968
UniProt
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWW6 Go to UniProtKB: Q5ZWW6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZWW6
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a isoform 1	T [auth a]	838	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P25286 (Rattus norvegicus) Explore P25286 Go to UniProtKB: P25286
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25286
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a	U [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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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit S1	V [auth c]	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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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit	W [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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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e 2	X [auth e]	81	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q5EB76 (Rattus norvegicus) Explore Q5EB76 Go to UniProtKB: Q5EB76
Entity Groups
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: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease K	Y [auth f]	98	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for D3ZIM6 (Rattus norvegicus) Explore D3ZIM6 Go to UniProtKB: D3ZIM6
Entity Groups
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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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 16 kDa proteolipid subunit	AA [auth h] BA [auth i] CA [auth j] DA [auth k] EA [auth l] AA [auth h], BA [auth i], CA [auth j], DA [auth k], EA [auth l], FA [auth m], GA [auth n], HA [auth o], Z [auth g]	155	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P63081 (Rattus norvegicus) Explore P63081 Go to UniProtKB: P63081
Entity Groups
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: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin receptor	IA [auth p]	350	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q6AXS4 (Rattus norvegicus) Explore Q6AXS4 Go to UniProtKB: Q6AXS4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6AXS4
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Reference Sequence

Small Molecules

Ligands 1 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 JA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain JA [auth C]	JA [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain JA [auth C] Interactions & Density Focus chain JA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-22

Deposition Author(s):

Rubinstein, J.L.

Abbas, Y.M.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2023-11-22
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.

7UZF | pdb_00007uzf

Rat Kidney V-ATPase with SidK, State 1

Literature

Structure of V-ATPase with NCOA7B

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

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Sequence Annotations

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Entity ID: 11

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Entity ID: 16

UniProt

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Entity ID: 17

UniProt

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data