9MOY | pdb_00009moy

Reconstituted yeast V-ATPase bound to Rtc5p

PDB DOI: https://doi.org/10.2210/pdb9MOY/pdb
EM Map EMD-48491: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-28 Released: 2026-04-08
Deposition Author(s): Wilkens, S., Khan, M.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

TLDc Protein Rtc5p Assembles Yeast V-ATPase

Wilkens, S., Khan, M.M.

To be published.

Macromolecule Content

Total Structure Weight: 1,054.23 kDa
Atom Count: 68,913
Modeled Residue Count: 8,847
Deposited Residue Count: 9,519
Unique protein chains: 17

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)-transporting two-sector ATPase	A, B [auth C], C [auth E]	617	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for B3LH69 (Saccharomyces cerevisiae (strain RM11-1a)) Explore B3LH69 Go to UniProtKB: B3LH69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3LH69
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 E	D [auth G], F [auth I], H [auth K]	233	Saccharomyces cerevisiae	Mutation(s): 0
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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit G	E [auth H], G [auth J], I [auth L]	114	Saccharomyces cerevisiae	Mutation(s): 0
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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit D	J [auth M]	256	Saccharomyces cerevisiae	Mutation(s): 0
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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit F	K [auth N]	118	Saccharomyces cerevisiae	Mutation(s): 0
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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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit C	L [auth O]	392	Saccharomyces cerevisiae	Mutation(s): 0
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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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Restriction of telomere capping protein 5	M [auth R]	567	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RTC5, SCRG_01514
UniProt
Find proteins for B3LJG1 (Saccharomyces cerevisiae (strain RM11-1a)) Explore B3LJG1 Go to UniProtKB: B3LJG1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3LJG1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit d	N [auth S]	345	Saccharomyces cerevisiae	Mutation(s): 0
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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c''	O [auth T]	213	Saccharomyces cerevisiae	Mutation(s): 0
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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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c'	P [auth U]	164	Saccharomyces cerevisiae	Mutation(s): 0
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
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit c	Q [auth V] R [auth W] S [auth X] T [auth Y] U [auth Z] Q [auth V], R [auth W], S [auth X], T [auth Y], U [auth Z], V [auth a], W [auth b], X [auth c]	160	Saccharomyces cerevisiae	Mutation(s): 0
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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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit e	Y [auth d]	73	Saccharomyces cerevisiae	Mutation(s): 0
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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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
V0 assembly protein 1	Z [auth e]	265	Saccharomyces cerevisiae	Mutation(s): 0
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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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Yeast V-ATPase subunit f	AA [auth f]	85	Saccharomyces cerevisiae	Mutation(s): 0
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
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit B	BA [auth B], CA [auth D], DA [auth F]	517	Saccharomyces cerevisiae	Mutation(s): 0
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: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit H	EA [auth P]	478	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41807 Go to UniProtKB: P41807
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41807
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type proton ATPase subunit a, vacuolar isoform	FA [auth Q]	840	Saccharomyces cerevisiae	Mutation(s): 0
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

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-08

Deposition Author(s):

Wilkens, S.

Khan, M.M.

Funding Organization	Location	Grant Number
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: 2026-04-08
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.

9MOY | pdb_00009moy

Reconstituted yeast V-ATPase bound to Rtc5p

Literature

TLDc Protein Rtc5p Assembles Yeast V-ATPase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

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Sequence Annotations

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 14

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data