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- PDB-3j9t: Yeast V-ATPase state 1 -

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Basic information

Entry
Database: PDB / ID: 3j9t
TitleYeast V-ATPase state 1
Components
  • (V-type proton ATPase subunit ...) x 10
  • V-type proton ATPase catalytic subunit A
KeywordsHYDROLASE / V-ATPase / V-type ATPase / vacuolar-type ATPase / proton pump
Function / homology
Function and homology information


vacuole-mitochondrion membrane contact site / protein localization to vacuolar membrane / cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly ...vacuole-mitochondrion membrane contact site / protein localization to vacuolar membrane / cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / pexophagy / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / protein targeting to vacuole / vacuole organization / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / intein-mediated protein splicing / intron homing / cellular hyperosmotic response / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / ATP metabolic process / H+-transporting two-sector ATPase / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / transmembrane transport / intracellular calcium ion homeostasis / endocytosis / cytoplasmic stress granule / ATPase binding / protein-containing complex assembly / endonuclease activity / intracellular iron ion homeostasis / Hydrolases; Acting on ester bonds / membrane raft / Golgi membrane / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / 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 C ...Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / 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 C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / Intein / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / 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 / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / 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 / Intein N-terminal splicing region / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / 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 N-term extension / 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 / 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 / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit B / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E / 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 F / V-type proton ATPase subunit H / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsZhao, J. / Benlekbir, S. / Rubinstein, J.L.
CitationJournal: Nature / Year: 2015
Title: Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase.
Authors: Jianhua Zhao / Samir Benlekbir / John L Rubinstein /
Abstract: Eukaryotic vacuolar H(+)-ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of ATP to ADP to pump protons across membranes and control the pH of many intracellular compartments. ...Eukaryotic vacuolar H(+)-ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of ATP to ADP to pump protons across membranes and control the pH of many intracellular compartments. ATP hydrolysis in the soluble catalytic region of the enzyme is coupled to proton translocation through the membrane-bound region by rotation of a central rotor subcomplex, with peripheral stalks preventing the entire membrane-bound region from turning with the rotor. The eukaryotic V-ATPase is the most complex rotary ATPase: it has three peripheral stalks, a hetero-oligomeric proton-conducting proteolipid ring, several subunits not found in other rotary ATPases, and is regulated by reversible dissociation of its catalytic and proton-conducting regions. Studies of ATP synthases, V-ATPases, and bacterial/archaeal V/A-ATPases have suggested that flexibility is necessary for the catalytic mechanism of rotary ATPases, but the structures of different rotational states have never been observed experimentally. Here we use electron cryomicroscopy to obtain structures for three rotational states of the V-ATPase from the yeast Saccharomyces cerevisiae. The resulting series of structures shows ten proteolipid subunits in the c-ring, setting the ATP:H(+) ratio for proton pumping by the V-ATPase at 3:10, and reveals long and highly tilted transmembrane α-helices in the a-subunit that interact with the c-ring. The three different maps reveal the conformational changes that occur to couple rotation in the symmetry-mismatched soluble catalytic region to the membrane-bound proton-translocating region. Almost all of the subunits of the enzyme undergo conformational changes during the transitions between these three rotational states. The structures of these states provide direct evidence that deformation during rotation enables the smooth transmission of power through rotary ATPases.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
A: V-type proton ATPase catalytic subunit A
B: V-type proton ATPase subunit B
C: V-type proton ATPase catalytic subunit A
D: V-type proton ATPase subunit B
E: V-type proton ATPase catalytic subunit A
F: V-type proton ATPase subunit B
Q: V-type proton ATPase subunit d
L: V-type proton ATPase subunit G
K: V-type proton ATPase subunit E
P: V-type proton ATPase subunit H
b: V-type proton ATPase subunit a, vacuolar isoform
O: V-type proton ATPase subunit C
H: V-type proton ATPase subunit G
G: V-type proton ATPase subunit E
J: V-type proton ATPase subunit G
I: V-type proton ATPase subunit E
Y: V-type proton ATPase subunit c
R: V-type proton ATPase subunit c
U: V-type proton ATPase subunit c
V: V-type proton ATPase subunit c
T: V-type proton ATPase subunit c
W: V-type proton ATPase subunit c
S: V-type proton ATPase subunit c
X: V-type proton ATPase subunit c
Z: V-type proton ATPase subunit c
a: V-type proton ATPase subunit c


Theoretical massNumber of molelcules
Total (without water)934,64328
Polymers934,64328
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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V-type proton ATPase subunit ... , 10 types, 25 molecules MNBDFQLHJKGIPbOYRUVTWSXZa

#1: 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) / Strain: SABY31 / References: UniProt: P32610
#2: 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) / Strain: SABY31 / References: UniProt: P39111
#4: 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) / Strain: SABY31 / References: UniProt: P16140
#5: 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) / Strain: SABY31 / References: UniProt: P32366
#6: 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 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: SABY31 / References: UniProt: P48836
#7: 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) / Strain: SABY31 / References: UniProt: P22203
#8: 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) / Strain: SABY31 / References: UniProt: P41807
#9: 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) / Strain: SABY31 / References: UniProt: P32563
#10: 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) / Strain: SABY31 / References: UniProt: P31412
#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.: 10 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: SABY31 / References: UniProt: P25515

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Protein , 1 types, 3 molecules ACE

#3: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / Vacuolar proton pump subunit A / Endonuclease PI-SceI / Sce VMA intein / VMA1- ...V-ATPase subunit A / Vacuolar proton pump subunit A / Endonuclease PI-SceI / Sce VMA intein / VMA1-derived endonuclease / VDE


Mass: 67665.305 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: SABY31
References: UniProt: P17255, H+-transporting two-sector ATPase, Hydrolases; Acting on ester bonds

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Details

Sequence detailsCHAINS A, C, AND E CONTAIN RESIDUES 2-283 and 738-1071 OF UNP P17255 WITH RESIDUES 284-737 REMOVED.

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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: Vacuolar-type ATPase / Type: COMPLEX
Details: A3B3CDE3FG3HadcXc'Yc''Z where X, Y, and Z indicate unknown stoichiometry and X+Y+Z=10
Molecular weightValue: 0.9 MDa / Experimental value: YES
Buffer solutionName: 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
pH: 7.4
Details: 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Homemade holey carbon on 400 square mesh Cu/Rh grid, glow-discharged 2 mins
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temp: 77 K / Humidity: 100 %
Details: Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Method: Blot for 23 seconds before freezing

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Oct 19, 2013 / Details: K2 Summit in counting mode, 2 frames/s for 15 s
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 34483 X / Calibrated magnification: 34483 X / Nominal defocus max: 7000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / Astigmatism: Manually corrected by inspecting FFT
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 77 K
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) / Details: K2 Summit in counting mode
Image scansNum. digital images: 3685
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2UCSF Chimeramodel fitting
3TMaCSparticle selection
4RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Maximum likelihood / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50503 / Nominal pixel size: 1.45 Å / Actual pixel size: 1.45 Å
Details: (Single particle details: Particles automatically selected using TMaCS and processed in Relion.) (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: REFINEMENT PROTOCOL--flexible DETAILS--Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
11U7L

1u7l

A1U7L1
21HO8

1ho8

A1HO82
34RND

4rnd

A4RND3
44RND

4rnd

B4RND3
54DL0

4dl0

E4DL04
64DL0

4dl0

G4DL04
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms57659 0 0 0 57659

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