7FDC | pdb_00007fdc

CryoEM Structures of Reconstituted V-ATPase, state3

PDB DOI: https://doi.org/10.2210/pdb7FDC/pdb
EM Map EMD-31540: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Saccharomyces cerevisiae S288C, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2021-07-16 Released: 2021-12-22
Deposition Author(s): Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., KIm, H., Wilkens, S., Roh, S.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

CryoEM Structures of Reconstituted V-ATPase and Oxr1-bound V1 Reveal a Novel Mechanism of Regulation.

Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., Kim, H., Wilkens, S., Roh, S.H.

(2021) EMBO J

Macromolecule Content

Total Structure Weight: 991.83 kDa
Atom Count: 64,497
Modeled Residue Count: 8,295
Deposited Residue Count: 8,967
Unique protein chains: 16

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Yeast Vacuolar ATPase A subunit	A, C, E	617	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 7.1.2.2 Membrane Entity: Yes
UniProt
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17255 Go to UniProtKB: P17255
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17255
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit B	B, D, F	517	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16140 Go to UniProtKB: P16140
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16140
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 E	G, I, K	233	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22203 Go to UniProtKB: P22203
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22203
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit G	H, J, L	122	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48836 Go to UniProtKB: P48836
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48836
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit D	M	256	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P32610 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32610 Go to UniProtKB: P32610
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32610
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit F	N	118	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39111 Go to UniProtKB: P39111
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39111
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit C	O	392	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VMA5 Membrane Entity: Yes
UniProt
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31412 Go to UniProtKB: P31412
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31412
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)	P	469	Saccharomyces cerevisiae S288C, Homo sapiens This entity is chimeric	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41807 Go to UniProtKB: P41807
Find proteins for Q9UI12 (Homo sapiens) Explore Q9UI12 Go to UniProtKB: Q9UI12
PHAROS: Q9UI12 GTEx: ENSG00000047249
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P41807 Q9UI12
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Yeast Vacuolar ATPase a subunit	Q	840	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32563 Go to UniProtKB: P32563
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32563
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit d	R [auth S]	345	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32366 Go to UniProtKB: P32366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32366
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c''	S [auth T]	213	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23968 Go to UniProtKB: P23968
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23968
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c'	T [auth U]	164	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32842 Go to UniProtKB: P32842
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32842
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c	AA [auth b] BA [auth c] U [auth V] V [auth W] W [auth X] AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	160	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25515 Go to UniProtKB: P25515
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25515
Sequence Annotations Expand
Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e	CA [auth d]	73	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7B6 Go to UniProtKB: Q3E7B6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3E7B6
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Reference Sequence

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| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
V0 assembly protein 1	DA [auth e]	265	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53262 Go to UniProtKB: P53262
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53262
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Yeast Vacuolar ATPase f subunit	EA [auth f]	85	Saccharomyces cerevisiae S288C	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C5R9 Go to UniProtKB: P0C5R9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C5R9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM058600
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA228340
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM141908

Revision History (Full details and data files)

Version 1.0: 2021-12-22
Type: Initial release
Version 1.1: 2024-06-12
Changes: Data collection

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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.

7FDC | pdb_00007fdc

CryoEM Structures of Reconstituted V-ATPase, state3

Literature

CryoEM Structures of Reconstituted V-ATPase and Oxr1-bound V1 Reveal a Novel Mechanism of Regulation.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

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Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)