Macromolecule Content

Total Structure Weight: 1095.89 kDa
Atom Count: 62385
Residue Count: 8454
Unique protein chains: 16

6VQ6

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)

DOI: 10.2210/pdb6VQ6/pdb
EMDataResource: EMD-21317

Classification: PROTON TRANSPORT
Organism(s): Rattus norvegicus, Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-04 Released: 2020-03-18
Deposition Author(s): Abbas, Y.M., Rubinstein, J.L.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation3D Report Full Report

Literature

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)

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

To be published.

Macromolecules

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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 Gene Names: Atp6v1a, rCG_52629 EC: 7.1.2.2
Find proteins for D4A133 (Rattus norvegicus) Explore D4A133 Go to UniProtKB: D4A133
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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 Gene Names: Atp6v1b2, Atp6b2, Vat2
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P62815 (Rattus norvegicus) Explore P62815 Go to UniProtKB: P62815
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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 Gene Names: Atp6v1c1
Find proteins for Q5FVI6 (Rattus norvegicus) Explore Q5FVI6 Go to UniProtKB: Q5FVI6
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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 Gene Names: Atp6v1d, rCG_61537
Find proteins for Q6P503 (Rattus norvegicus) Explore Q6P503 Go to UniProtKB: Q6P503
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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 Gene Names: Atp6v1e1
Find proteins for Q6PCU2 (Rattus norvegicus) Explore Q6PCU2 Go to UniProtKB: Q6PCU2
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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 Gene Names: Atp6v1f, Atp6s14, Vatf
Find proteins for P50408 (Rattus norvegicus) Explore P50408 Go to UniProtKB: P50408
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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 Gene Names: Atp6v1g2, Aif1, Bat1a, Cdk2ap1-ps2, Cdk2ap1-ps3, Cdk2ap1-ps4, Cdk2ap1-ps5, Cdk2ap1-ps6, E230034O05Rik, LOC224733l-3... Atp6v1g2, Aif1, Bat1a, Cdk2ap1-ps2, Cdk2ap1-ps3, Cdk2ap1-ps4, Cdk2ap1-ps5, Cdk2ap1-ps6, E230034O05Rik, LOC224733l-3, LOC224733l-4, LOC224733l-5, LOC224733l-6, LOC224733l-7, LOC224733l-8, Lst1, RT1-CE12, RT1-CE3, RT1-CE5, RT1-CE6, RT1-CE8, RT1-CE9, Sacm2l-ps3, Sacm2l-ps4, Sacm2l-ps5, Sacm2l-ps6, Sacm2l-ps7, Tnf, rCG_38311
Find proteins for Q8R2H0 (Rattus norvegicus) Explore Q8R2H0 Go to UniProtKB: Q8R2H0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Effector protein SidK	Q, R, S	301	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: lpg0968
Find proteins for Q5ZWW6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWW6 Go to UniProtKB: Q5ZWW6
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 116 kDa subunit a isoform 1	a	838	Rattus norvegicus	Mutation(s): 0 Gene Names: Atp6v0a1, Atp6n1, Vpp1
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P25286 (Rattus norvegicus) Explore P25286 Go to UniProtKB: P25286
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a	b	205	Rattus norvegicus	Mutation(s): 0 Gene Names: Atp6v0b, Atp6v0b_predicted, rCG_50448
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for B0K022 (Rattus norvegicus) Explore B0K022 Go to UniProtKB: B0K022
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit S1	c	463	Rattus norvegicus	Mutation(s): 0 Gene Names: Atp6ap1, Atp6ip1, Atp6s1
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for O54715 (Rattus norvegicus) Explore O54715 Go to UniProtKB: O54715
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit	d	351	Rattus norvegicus	Mutation(s): 0 Gene Names: Atp6v0d1, rCG_51062
Find proteins for Q5M7T6 (Rattus norvegicus) Explore Q5M7T6 Go to UniProtKB: Q5M7T6
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e 2	e	81	Rattus norvegicus	Mutation(s): 0 Gene Names: Atp6v0e2
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for Q5EB76 (Rattus norvegicus) Explore Q5EB76 Go to UniProtKB: Q5EB76
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease K	f	98	Rattus norvegicus	Mutation(s): 0 Gene Names: Rnasek
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for D3ZIM6 (Rattus norvegicus) Explore D3ZIM6 Go to UniProtKB: D3ZIM6
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase 16 kDa proteolipid subunit	g, h, i, j, k, l, m, n, o	155	Rattus norvegicus	Mutation(s): 0 Gene Names: Atp6v0c, Atp6c, Atp6l, Atpl
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for P63081 (Rattus norvegicus) Explore P63081 Go to UniProtKB: P63081
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin receptor	p	350	Rattus norvegicus	Mutation(s): 0 Gene Names: Atp6ap2, Atp6ip2
Membrane protein Mpstruc	Group: TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: Vacuolar ATPase (V-ATPase)	Protein: V-ATPase, composite model rotational state 1 bound to ADP & SidK
Find proteins for Q6AXS4 (Rattus norvegicus) Explore Q6AXS4 Go to UniProtKB: Q6AXS4
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Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download CCD File	C	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Ligand Interaction
MG Query on MG Download CCD File	C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Deposited Date: 2020-02-04
Released Date: 2020-03-18

Deposition Author(s):

Abbas, Y.M.

Rubinstein, J.L.

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

Revision History

Version 1.0: 2020-03-18
Type: Initial release

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169117 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

6VQ6

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)

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Experimental Data

Structure Validation

Deposition Data

Revision History