7FDC

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  OPMPDBTM


• 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)

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Experimental Data Snapshot

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

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 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 31-mer - A8B3C3D3E3F1G1H1I1J1K1L1M1N1O1P1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 31-mer - A10B6C3D3E1F1G1H1I1J1K1L1M1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 12-mer - B3C3D3E3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 12-mer - B3C3D3E3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

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

Macromolecules

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 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 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 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 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 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 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 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
UniProt Groups	P41807Q9UI12

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 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 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 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 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], 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 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 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 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

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

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Khan, M.M., Lee, S., Oot, R.A., Couoh-Cardel, S., KIm, H., Wilkens, S., Roh, S.H.

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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  

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