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- PDB-9nn1: Yeast V1-ATPase bound to Rtc5p -

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Basic information

Entry
Database: PDB / ID: 9nn1
TitleYeast V1-ATPase bound to Rtc5p
Components
  • (V-type proton ATPase subunit ...) x 4
  • H(+)-transporting two-sector ATPase
  • Restriction of telomere capping protein 5
  • Yeast V-ATPase subunit G
KeywordsPROTON TRANSPORT / Vacuolar ATPase / V1-ATPase / Rtc5p / protein structure
Function / homology
Function and homology information


vacuole-mitochondrion membrane contact site / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification ...vacuole-mitochondrion membrane contact site / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / pexophagy / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / proton-transporting ATPase activity, rotational mechanism / ATP metabolic process / H+-transporting two-sector ATPase / Neutrophil degranulation / proton transmembrane transport / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / response to oxidative stress / membrane raft / Golgi membrane / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit ...TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase catalytic subunit A / Restriction of telomere capping protein 5 / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit D / V-type proton ATPase subunit F
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKhan, M.M. / Wilkens, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141908 United States
CitationJournal: To Be Published
Title: TLDc Protein Rtc5p Assembles Yeast V-ATPase
Authors: Khan, M.M. / Wilkens, S.
History
DepositionMar 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H(+)-transporting two-sector ATPase
C: H(+)-transporting two-sector ATPase
E: H(+)-transporting two-sector ATPase
G: V-type proton ATPase subunit E
H: Yeast V-ATPase subunit G
I: V-type proton ATPase subunit E
J: Yeast V-ATPase subunit G
K: V-type proton ATPase subunit E
L: Yeast V-ATPase subunit G
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
R: Restriction of telomere capping protein 5
B: V-type proton ATPase subunit B
D: V-type proton ATPase subunit B
F: V-type proton ATPase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)605,07716
Polymers604,64915
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 7 molecules ACEHJLR

#1: Protein H(+)-transporting two-sector ATPase


Mass: 67796.508 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: B3LH69, H+-transporting two-sector ATPase
#3: Protein Yeast V-ATPase subunit G


Mass: 13735.680 Da / Num. of mol.: 3 / Mutation: N-terminal FLAG tag / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#6: Protein Restriction of telomere capping protein 5


Mass: 64368.312 Da / Num. of mol.: 1 / Mutation: N-terminal His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RTC5, SCRG_01514 / Production host: Escherichia coli (E. coli) / References: UniProt: B3LJG1

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V-type proton ATPase subunit ... , 4 types, 8 molecules GIKMNBDF

#2: Protein V-type proton ATPase subunit E / V-ATPase subunit E / V-ATPase 27 kDa subunit / Vacuolar proton pump subunit E


Mass: 26508.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22203
#4: Protein V-type proton ATPase subunit D / V-ATPase subunit D / Vacuolar proton pump subunit D


Mass: 29235.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32610
#5: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13479.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39111
#7: Protein V-type proton ATPase subunit B / V-ATPase subunit B / V-ATPase 57 kDa subunit / Vacuolar proton pump subunit B


Mass: 57815.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16140

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast V1-ATPase bound to Rtc5p / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 0.6 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 279 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 49.25 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7ISOLDEmodel fitting
8Cootmodel fitting
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
14PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 556655
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67351 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17tmm

7tmm

17tmm1PDBexperimental model
29moy

9moy
PDB Unreleased entry

19moy2PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 145.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002639526
ELECTRON MICROSCOPYf_angle_d0.468853401
ELECTRON MICROSCOPYf_chiral_restr0.03946009
ELECTRON MICROSCOPYf_plane_restr0.00336943
ELECTRON MICROSCOPYf_dihedral_angle_d5.42125373

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