6M0R

2.7A Yeast Vo state3

PDB DOI: https://doi.org/10.2210/pdb6M0R/pdb
EM Map EMD-30034: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2020-02-22 Released: 2020-11-04
Deposition Author(s): Roh, S.H., Shekhar, M., Pintilie, G., Chipot, C., Wilkens, S., Singharoy, A., Chiu, W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Research Foundation (NRF, Korea), National Science Foundation (NSF, United States), Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 346.83 kDa
Atom Count: 23,667
Modelled Residue Count: 2,915
Deposited Residue Count: 2,990
Unique protein chains: 8

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c'	A [auth D]	158	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VMA11, CLS9, TFP3, YPL234C, P1064 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32842
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c''	B [auth C]	198	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VMA16, PPA1, YHR026W 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23968
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V0 assembly protein 1	C [auth N]	52	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VOA1, YGR106C 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53262
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e	D [auth M]	71	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VMA9, CWH36, LDB10, YCL005W-A 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3E7B6
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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 c	E G [auth F] H [auth G] I [auth H] J [auth I] E, G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L]	159	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VMA3, CLS7, CUP5, GEF2, YEL027W 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25515
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YPR170W-B	F [auth O]	69	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: YPR170W-B 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C5R9
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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 d	N [auth B]	345	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VMA6, YLR447C, L9324.8 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32366
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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 a, vacuolar isoform	O [auth A]	825	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: VPH1, YOR270C 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32563
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P	5		N/A	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEE (Subject of Investigation/LOI) Query on PEE Download Ideal Coordinates CCD File SDF format, chain HA [auth H] SDF format, chain R [auth C] SDF format, chain AA [auth M] SDF format, chain BA [auth M] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth O] SDF format, chain FA [auth F] SDF format, chain GA [auth G] SDF format, chain IA [auth I] SDF format, chain JA [auth I] SDF format, chain KA [auth J] SDF format, chain LA [auth J] SDF format, chain MA [auth K] SDF format, chain NA [auth K] SDF format, chain OA [auth B] SDF format, chain PA [auth A] SDF format, chain Q [auth C] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain S [auth C] SDF format, chain SA [auth A] SDF format, chain T [auth C] SDF format, chain TA [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain HA [auth H] MOL2 format, chain R [auth C] MOL2 format, chain AA [auth M] MOL2 format, chain BA [auth M] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth O] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain KA [auth J] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth K] MOL2 format, chain NA [auth K] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth A] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	AA [auth M] BA [auth M] CA [auth E] DA [auth E] EA [auth O] AA [auth M], BA [auth M], CA [auth E], DA [auth E], EA [auth O], FA [auth F], GA [auth G], HA [auth H], IA [auth I], JA [auth I], KA [auth J], LA [auth J], MA [auth K], NA [auth K], OA [auth B], PA [auth A], Q [auth C], QA [auth A], R [auth C], RA [auth A], S [auth C], SA [auth A], T [auth C], TA [auth A], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AA [auth M] Focus chain BA [auth M] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth O] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain HA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth K] Focus chain OA [auth B] Focus chain PA [auth A] Focus chain Q [auth C] Focus chain QA [auth A] Focus chain R [auth C] Focus chain RA [auth A] Focus chain S [auth C] Focus chain SA [auth A] Focus chain T [auth C] Focus chain TA [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth M] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth O] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain HA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth K] Focus chain OA [auth B] Focus chain PA [auth A] Focus chain Q [auth C] Focus chain QA [auth A] Focus chain R [auth C] Focus chain RA [auth A] Focus chain S [auth C] Focus chain SA [auth A] Focus chain T [auth C] Focus chain TA [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
EYR Query on EYR Download Ideal Coordinates CCD File SDF format, chain VA [auth A] MOL2 format, chain VA [auth A]	VA [auth A]	(6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene C₄₀ H₆₈ NNAMSNGZQLVMQY-GAPQENEMSA-N		Interactions Focus chain VA [auth A] Interactions & Density Focus chain VA [auth A]
PPV Query on PPV Download Ideal Coordinates CCD File SDF format, chain UA [auth A] MOL2 format, chain UA [auth A]	UA [auth A]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain UA [auth A] Interactions & Density Focus chain UA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM058600
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM079429
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10OD021600
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019M3E5D6063865
National Science Foundation (NSF, United States)	United States	MCB-1942763
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM067887
Agence Nationale de la Recherche (ANR)	France	ProteaseInAction Grant

Revision History (Full details and data files)

Version 1.0: 2020-11-04
Type: Initial release
Version 2.0: 2024-03-27
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

6M0R

2.7A Yeast Vo state3

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

Entity Groups

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

Entity Groups

Sequence Annotations

Entity ID: 9

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)