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- PDB-9odu: Yeast V-ATPase bound to Rtc5p, rotary state 2 -

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Basic information

Entry
Database: PDB / ID: 9odu
TitleYeast V-ATPase bound to Rtc5p, rotary state 2
Components
  • (V-type proton ATPase subunit ...) x 13
  • H(+)-transporting two-sector ATPase
  • Restriction of telomere capping protein 5
  • V0 assembly protein 1
  • Yeast V-ATPase subunit f
KeywordsPROTON TRANSPORT / Vacuolar ATPase / Rtc5p / TLDc domain / protein structure
Function / homology
Function and homology information


vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes ...vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Golgi lumen acidification / Amino acids regulate mTORC1 / proteasome storage granule assembly / P-type proton-exporting transporter activity / vacuolar transport / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuole organization / proton-transporting V-type ATPase complex / fungal-type vacuole / protein targeting to vacuole / vacuolar proton-transporting V-type ATPase complex / pexophagy / cellular hyperosmotic response / vacuolar acidification / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / proton-transporting ATPase activity, rotational mechanism / intracellular copper ion homeostasis / H+-transporting two-sector ATPase / ATP metabolic process / Neutrophil degranulation / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / endocytosis / ATPase binding / protein-containing complex assembly / response to oxidative stress / intracellular iron ion homeostasis / membrane raft / Golgi membrane / endoplasmic reticulum 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 H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A ...TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Ribonuclease kappa / : / V-type proton ATPase subunit f-like / Vacuolar (H+)-ATPase G subunit / V-type proton ATPase subunit S1/VOA1, transmembrane domain / Vacuolar (H+)-ATPase G subunit / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / 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 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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 / Armadillo-like helical / Armadillo-type fold / 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 f / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit C / V-type proton ATPase subunit d ...ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase catalytic subunit A / Restriction of telomere capping protein 5 / V-type proton ATPase subunit f / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit C / V-type proton ATPase subunit d / V-type proton ATPase subunit a, vacuolar isoform / V-type proton ATPase subunit D / V-type proton ATPase subunit c' / V-type proton ATPase subunit F / V-type proton ATPase subunit H / V-type proton ATPase subunit G / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWilkens, S. / Khan, M.M.
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: Yeast V-ATPase bound to Rtc5p, rotary state 2
Authors: Wilkens, S. / Khan, M.M.
History
DepositionApr 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 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

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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: V-type proton ATPase subunit G
I: V-type proton ATPase subunit E
J: V-type proton ATPase subunit G
K: V-type proton ATPase subunit E
L: V-type proton ATPase subunit G
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
O: V-type proton ATPase subunit C
R: Restriction of telomere capping protein 5
S: V-type proton ATPase subunit d
T: V-type proton ATPase subunit c''
U: V-type proton ATPase subunit c'
V: V-type proton ATPase subunit c
W: V-type proton ATPase subunit c
X: V-type proton ATPase subunit c
Y: V-type proton ATPase subunit c
Z: V-type proton ATPase subunit c
a: V-type proton ATPase subunit c
b: V-type proton ATPase subunit c
c: V-type proton ATPase subunit c
d: V-type proton ATPase subunit e
e: V0 assembly protein 1
f: Yeast V-ATPase subunit f
P: V-type proton ATPase subunit H
Q: V-type proton ATPase subunit a, vacuolar isoform
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)1,054,22633
Polymers1,053,79932
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 , 4 types, 6 molecules ACERef

#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
#7: Protein Restriction of telomere capping protein 5


Mass: 64368.312 Da / Num. of mol.: 1 / Mutation: N-terminal 6xHis 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
#13: Protein V0 assembly protein 1


Mass: 29694.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53262
#14: Protein Yeast V-ATPase subunit f


Mass: 9369.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C5R9

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V-type proton ATPase subunit ... , 13 types, 26 molecules GIKHJLMNOSTUVWXYZabcdPQBDF

#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
#3: Protein V-type proton ATPase subunit G / V-ATPase subunit G / V-ATPase 13 kDa subunit / Vacuolar proton pump subunit G


Mass: 12738.706 Da / Num. of mol.: 3 / Mutation: N-terminal FLAG tag / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48836
#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
#6: Protein V-type proton ATPase subunit C / V-ATPase subunit C / V-ATPase 42 kDa subunit / Vacuolar proton pump subunit C


Mass: 44241.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P31412
#8: Protein V-type proton ATPase subunit d / V-ATPase subunit d / V-ATPase 39 kDa subunit / V-ATPase subunit M39 / Vacuolar proton pump subunit d


Mass: 39822.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32366
#9: Protein V-type proton ATPase subunit c'' / V-ATPase subunit c'' / V-ATPase 22 kDa proteolipid subunit / Vacuolar proton pump c'' subunit


Mass: 22610.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23968
#10: Protein V-type proton ATPase subunit c' / V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase ...V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase 16 kDa proteolipid subunit 2 / Vacuolar proton pump c' subunit


Mass: 17046.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32842
#11: Protein
V-type proton ATPase subunit c / V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / ...V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / Vacuolar proton pump c subunit


Mass: 16357.501 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25515
#12: Protein V-type proton ATPase subunit e / V-ATPase subunit e / Low dye-binding protein 10 / Vacuolar proton pump subunit e


Mass: 8387.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7B6
#15: Protein V-type proton ATPase subunit H / V-ATPase subunit H / V-ATPase 54 kDa subunit / Vacuolar proton pump subunit H


Mass: 54482.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41807
#16: Protein V-type proton ATPase subunit a, vacuolar isoform / V-ATPase a 1 subunit / V-ATPase 95 kDa subunit / Vacuolar pH protein 1 / Vacuolar proton pump a ...V-ATPase a 1 subunit / V-ATPase 95 kDa subunit / Vacuolar pH protein 1 / Vacuolar proton pump a subunit / Vacuolar proton translocating ATPase subunit a 1


Mass: 95625.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32563
#17: 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

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


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

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Details

Has ligand of interestY
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 V-ATPase bound to Rtc5p, rotary state 2 / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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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) / Num. of real images: 3561

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
7ISOLDEmodel fitting
8Cootmodel fitting
9UCSF ChimeraXmodel fitting
11RELION5initial Euler assignment
12RELION5final Euler assignment
14RELION53D reconstruction
15PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 558587
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58688 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17fdb

7fdb

17fdb1PDBexperimental model
29nn1

9nn1

19nn12PDBexperimental model
39moy

9moy

19moy3PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 156.59 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002570331
ELECTRON MICROSCOPYf_angle_d0.44895159
ELECTRON MICROSCOPYf_chiral_restr0.036710952
ELECTRON MICROSCOPYf_plane_restr0.003212154
ELECTRON MICROSCOPYf_dihedral_angle_d5.03589547

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