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- EMDB-31538: CryoEM Structure of Reconstituted V-ATPase, state1 -

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Basic information

Entry
Database: EMDB / ID: EMD-31538
TitleCryoEM Structure of Reconstituted V-ATPase, state1
Map datastate1_postprocess
Sample
  • Complex: Yeast Vacuolar ATPase in rotary state 1
    • Complex: Yeast V-type proton ATPase subunit C
      • Protein or peptide: x 1 types
    • Complex: Chimeric subunit H
      • Protein or peptide: x 1 types
    • Complex: V-type proton ATPase subunits
      • Protein or peptide: x 14 types
KeywordsATPase / proton pump / rotary motor enzyme / membrane protein / MOTOR PROTEIN
Function / homology
Function and homology information


Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / Nef Mediated CD8 Down-regulation / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH ...Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / Nef Mediated CD8 Down-regulation / ATPase-coupled ion transmembrane transporter activity / 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 / synaptic vesicle lumen acidification / Transferrin endocytosis and recycling / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane / lysosomal lumen acidification / 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 / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / ROS and RNS production in phagocytes / cellular hyperosmotic response / Nef Mediated CD4 Down-regulation / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / regulation of macroautophagy / enzyme regulator activity / ATP metabolic process / Insulin receptor recycling / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / endosome membrane / membrane raft / Golgi membrane / lysosomal membrane / endoplasmic reticulum membrane / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily ...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 / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / ATPase, V1 complex, subunit B / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V1 complex, subunit F, eukaryotic / 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-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / C-terminal domain of V and A type ATP synthase / 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 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 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 / V0 assembly protein 1 / V-type proton ATPase subunit e / V-type proton ATPase subunit H
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae S288C (yeast) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKhan MM / Lee S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM058600 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA228340 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141908 United States
CitationJournal: EMBO J / Year: 2022
Title: Oxidative stress protein Oxr1 promotes V-ATPase holoenzyme disassembly in catalytic activity-independent manner.
Authors: Md Murad Khan / Seowon Lee / Sergio Couoh-Cardel / Rebecca A Oot / Hyunmin Kim / Stephan Wilkens / Soung-Hun Roh /
Abstract: The vacuolar ATPase (V-ATPase) is a rotary motor proton pump that is regulated by an assembly equilibrium between active holoenzyme and autoinhibited V -ATPase and V proton channel subcomplexes. ...The vacuolar ATPase (V-ATPase) is a rotary motor proton pump that is regulated by an assembly equilibrium between active holoenzyme and autoinhibited V -ATPase and V proton channel subcomplexes. Here, we report cryo-EM structures of yeast V-ATPase assembled in vitro from lipid nanodisc reconstituted V and mutant V . Our analysis identified holoenzymes in three active rotary states, indicating that binding of V to V provides sufficient free energy to overcome V autoinhibition. Moreover, the structures suggest that the unequal spacing of V 's proton-carrying glutamic acid residues serves to alleviate the symmetry mismatch between V and V motors, a notion that is supported by mutagenesis experiments. We also uncover a structure of free V bound to Oxr1, a conserved but poorly characterized factor involved in the oxidative stress response. Biochemical experiments show that Oxr1 inhibits V -ATPase and causes disassembly of the holoenzyme, suggesting that Oxr1 plays a direct role in V-ATPase regulation.
History
DepositionJul 16, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7fda
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31538.png

Downloads & links

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Map

FileDownload / File: emd_31538.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstate1_postprocess
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.03753849 - 0.097617246
Average (Standard dev.)0.00044757995 (±0.0049826666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0380.0980.000

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Supplemental data

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Additional map: state1 vo masked refine

Fileemd_31538_additional_1.map
Annotationstate1_vo_masked_refine
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Additional map: state1 half2

Fileemd_31538_additional_2.map
Annotationstate1_half2
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Additional map: state1 half1

Fileemd_31538_additional_3.map
Annotationstate1_half1
Projections & Slices
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Additional map: state1 v1 masked refine

Fileemd_31538_additional_4.map
Annotationstate1_v1_masked_refine
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Additional map: chimera combined map

Fileemd_31538_additional_5.map
Annotationchimera_combined_map
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Sample components

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Entire : Yeast Vacuolar ATPase in rotary state 1

EntireName: Yeast Vacuolar ATPase in rotary state 1
Components
  • Complex: Yeast Vacuolar ATPase in rotary state 1
    • Complex: Yeast V-type proton ATPase subunit C
      • Protein or peptide: V-type proton ATPase subunit C
    • Complex: Chimeric subunit H
      • Protein or peptide: Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)
    • Complex: V-type proton ATPase subunits
      • Protein or peptide: Yeast Vacuolar ATPase A subunit
      • Protein or peptide: V-type proton ATPase subunit B
      • Protein or peptide: V-type proton ATPase subunit E
      • Protein or peptide: V-type proton ATPase subunit G
      • Protein or peptide: V-type proton ATPase subunit D
      • Protein or peptide: V-type proton ATPase subunit F
      • Protein or peptide: Yeast Vacuolar ATPase a subunit
      • Protein or peptide: V-type proton ATPase subunit d
      • Protein or peptide: V-type proton ATPase subunit c''
      • Protein or peptide: V-type proton ATPase subunit c'
      • Protein or peptide: V-type proton ATPase subunit c
      • Protein or peptide: V-type proton ATPase subunit e
      • Protein or peptide: V0 assembly protein 1
      • Protein or peptide: Yeast Vacuolar ATPase f subunit

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Supramolecule #1: Yeast Vacuolar ATPase in rotary state 1

SupramoleculeName: Yeast Vacuolar ATPase in rotary state 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 1 MDa

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Supramolecule #2: Yeast V-type proton ATPase subunit C

SupramoleculeName: Yeast V-type proton ATPase subunit C / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Supramolecule #3: Chimeric subunit H

SupramoleculeName: Chimeric subunit H / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8
Details: Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Supramolecule #4: V-type proton ATPase subunits

SupramoleculeName: V-type proton ATPase subunits / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1-#6, #9-#16 / Details: V-ATPase subunits purified from natural source

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Macromolecule #1: Yeast Vacuolar ATPase A subunit

MacromoleculeName: Yeast Vacuolar ATPase A subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 67.796508 KDa
SequenceString: MAGAIENARK EIKRISLEDH AESEYGAIYS VSGPVVIAEN MIGCAMYELV KVGHDNLVGE VIRIDGDKAT IQVYEETAGL TVGDPVLRT GKPLSVELGP GLMETIYDGI QRPLKAIKEE SQSIYIPRGI DTPALDRTIK WQFTPGKFQV GDHISGGDIY G SVFENSLI ...String:
MAGAIENARK EIKRISLEDH AESEYGAIYS VSGPVVIAEN MIGCAMYELV KVGHDNLVGE VIRIDGDKAT IQVYEETAGL TVGDPVLRT GKPLSVELGP GLMETIYDGI QRPLKAIKEE SQSIYIPRGI DTPALDRTIK WQFTPGKFQV GDHISGGDIY G SVFENSLI SSHKILLPPR SRGTITWIAP AGEYTLDEKI LEVEFDGKKS DFTLYHTWPV RVPRPVTEKL SADYPLLTGQ RV LDALFPC VQGGTTCIPG AFGCGKTVIS QSLSKYSNSD AIIYVGCGER GNEMAEVLME FPELYTEMSG TKEPIMKRTT LVA NTSNMP VAAREASIYT GITLAEYFRD QGKNVSMIAD SSSRWAEALR EISGRLGEMP ADQGFPAYLG AKLASFYERA GKAV ALGSP DRTGSVSIVA AVSPAGGDFS DPVTTATLGI TQVFWGLDKK LAQRKHFPSI NTSVSYSKYT NVLNKFYDSN YPEFP VLRD RMKEILSNAE ELEQVVQLVG KSALSDSDKI TLDVATLIKE DFLQQNGYST YDAFCPIWKT FDMMRAFISY HDEAQK AVA NGANWSKLAD STGDVKHAVS SSKFFEPSRG EKEVHGEFEK LLSTMQERFA ESTD

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Macromolecule #2: V-type proton ATPase subunit B

MacromoleculeName: V-type proton ATPase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 57.815023 KDa
SequenceString: MVLSDKELFA INKKAVEQGF NVKPRLNYNT VSGVNGPLVI LEKVKFPRYN EIVNLTLPDG TVRQGQVLEI RGDRAIVQVF EGTSGIDVK KTTVEFTGES LRIPVSEDML GRIFDGSGRP IDNGPKVFAE DYLDINGSPI NPYARIYPEE MISTGVSAID T MNSIARGQ ...String:
MVLSDKELFA INKKAVEQGF NVKPRLNYNT VSGVNGPLVI LEKVKFPRYN EIVNLTLPDG TVRQGQVLEI RGDRAIVQVF EGTSGIDVK KTTVEFTGES LRIPVSEDML GRIFDGSGRP IDNGPKVFAE DYLDINGSPI NPYARIYPEE MISTGVSAID T MNSIARGQ KIPIFSASGL PHNEIAAQIC RQAGLVRPTK DVHDGHEENF SIVFAAMGVN LETARFFKQD FEENGSLERT SL FLNLAND PTIERIITPR LALTTAEYLA YQTERHVLTI LTDMSSYADA LREVSAAREE VPGRRGYPGY MYTDLSTIYE RAG RVEGRN GSITQIPILT MPNDDITHPI PDLTGYITEG QIFVDRQLHN KGIYPPINVL PSLSRLMKSA IGEGMTRKDH GDVS NQLYA KYAIGKDAAA MKAVVGEEAL SIEDKLSLEF LEKFEKTFIT QGAYEDRTVF ESLDQAWSLL RIYPKEMLNR ISPKI LDEF YDRARDDADE DEEDPDTRSS GKKKDASQEE SLI

UniProtKB: V-type proton ATPase subunit B

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Macromolecule #3: V-type proton ATPase subunit E

MacromoleculeName: V-type proton ATPase subunit E / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 26.508393 KDa
SequenceString: MSSAITALTP NQVNDELNKM QAFIRKEAEE KAKEIQLKAD QEYEIEKTNI VRNETNNIDG NFKSKLKKAM LSQQITKSTI ANKMRLKVL SAREQSLDGI FEETKEKLSG IANNRDEYKP ILQSLIVEAL LKLLEPKAIV KALERDVDLI ESMKDDIMRE Y GEKAQRAP ...String:
MSSAITALTP NQVNDELNKM QAFIRKEAEE KAKEIQLKAD QEYEIEKTNI VRNETNNIDG NFKSKLKKAM LSQQITKSTI ANKMRLKVL SAREQSLDGI FEETKEKLSG IANNRDEYKP ILQSLIVEAL LKLLEPKAIV KALERDVDLI ESMKDDIMRE Y GEKAQRAP LEEIVISNDY LNKDLVSGGV VVSNASDKIE INNTLEERLK LLSEEALPAI RLELYGPSKT RKFFD

UniProtKB: V-type proton ATPase subunit E

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Macromolecule #4: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 13.73568 KDa
SequenceString:
MDYKDDDDKS QKNGIATLLQ AEKEAHEIVS KARKYRQDKL KQAKTDAAKE IDSYKIQKDK ELKEFEQKNA GGVGELEKKA EAGVQGELA EIKKIAEKKK DDVVKILIET VIKPSAEVHI NAL

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Macromolecule #5: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 29.235023 KDa
SequenceString: MSGNREQVFP TRMTLGLMKT KLKGANQGYS LLKRKSEALT KRFRDITKRI DDAKQKMGRV MQTAAFSLAE VSYATGENIG YQVQESVST ARFKVRARQE NVSGVYLSQF ESYIDPEIND FRLTGLGRGG QQVQRAKEIY SRAVETLVEL ASLQTAFIIL D EVIKVTNR ...String:
MSGNREQVFP TRMTLGLMKT KLKGANQGYS LLKRKSEALT KRFRDITKRI DDAKQKMGRV MQTAAFSLAE VSYATGENIG YQVQESVST ARFKVRARQE NVSGVYLSQF ESYIDPEIND FRLTGLGRGG QQVQRAKEIY SRAVETLVEL ASLQTAFIIL D EVIKVTNR RVNAIEHVII PRTENTIAYI NSELDELDRE EFYRLKKVQE KKQNETAKLD AEMKLKRDRA EQDASEVAAD EE PQGETLV ADQEDDVIF

UniProtKB: V-type proton ATPase subunit D

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Macromolecule #6: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 13.47917 KDa
SequenceString:
MAEKRTLIAV IADEDTTTGL LLAGIGQITP ETQEKNFFVY QEGKTTKEEI TDKFNHFTEE RDDIAILLIN QHIAENIRAR VDSFTNAFP AILEIPSKDH PYDPEKDSVL KRVRKLFGE

UniProtKB: V-type proton ATPase subunit F

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Macromolecule #7: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 44.241352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATALYTAND FILISLPQNA QPVTAPGSKT DSWFNETLIG GRAFVSDFKI PEFKIGSLDT LIVESEELSK VDNQIGASIG KIIEILQGL NETSTNAYRT LPINNMPVPE YLENFQWQTR KFKLDKSIKD LITLISNESS QLDADVRATY ANYNSAKTNL A AAERKKTG ...String:
MATALYTAND FILISLPQNA QPVTAPGSKT DSWFNETLIG GRAFVSDFKI PEFKIGSLDT LIVESEELSK VDNQIGASIG KIIEILQGL NETSTNAYRT LPINNMPVPE YLENFQWQTR KFKLDKSIKD LITLISNESS QLDADVRATY ANYNSAKTNL A AAERKKTG DLSVRSLHDI VKPEDFVLNS EHLTTVLVAV PKSLKSDFEK SYETLSKNVV PASASVIAED AEYVLFNVHL FK KNVQEFT TAAREKKFIP REFNYSEELI DQLKKEHDSA ASLEQSLRVQ LVRLAKTAYV DVFINWFHIK ALRVYVESVL RYG LPPHFN IKIIAVPPKN LSKCKSELID AFGFLGGNAF MKDKKGKINK QDTSLHQYAS LVDTEYEPFV MYIINL

UniProtKB: V-type proton ATPase subunit C

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Macromolecule #8: Fusion of yeast V-type proton ATPase subunit H(NT) and human V-ty...

MacromoleculeName: Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT)
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.885984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGATKILMDS THFNEIRSII RSRSVAWDAL ARSEELSEID ASTAKALESI LVKKNIGDGL SSSNNAHSGF KVNGKTLIPL IHLLSTSDN EDCKKSVQNL IAELLSSDKY GDDTVKFFQE DPKQLEQLFD VSLKGDFQTV LISGFNVVSL LVQNGLHNVK L VEKLLKNN ...String:
MGATKILMDS THFNEIRSII RSRSVAWDAL ARSEELSEID ASTAKALESI LVKKNIGDGL SSSNNAHSGF KVNGKTLIPL IHLLSTSDN EDCKKSVQNL IAELLSSDKY GDDTVKFFQE DPKQLEQLFD VSLKGDFQTV LISGFNVVSL LVQNGLHNVK L VEKLLKNN NLINILQNIE QMDTCYVCIR LLQELAVIPE YRDVIWLHEK KFMPTLFKIL QRATDSQLAT RIVATNSNHL GI QLQYHSL LLIWLLTFNP VFANELVQKY LSDFLDLLKL VKITIKEKVS RLCISIILQC CSTRVKQHKK VIKQLLLLGN ALP TVQSLS ERKYSDEELR QDISNLKEIL ENEYQELTSF DEYSSELKSG RLEWSPVHKS EKFWRENAVR LNEKNYELLK ILTK LLEVS DDPQVLAVAA HDVGEYVRHY PRGKRVIEQL GGKQLVMNHM HHEDQQVRYN ALLAVQKLMV HNWE

UniProtKB: V-type proton ATPase subunit H, V-type proton ATPase subunit H

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Macromolecule #9: Yeast Vacuolar ATPase a subunit

MacromoleculeName: Yeast Vacuolar ATPase a subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 95.625484 KDa
SequenceString: MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM ...String:
MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM IDANGENIAA AIGASVNYVT GVIARDKVAT LEQILWRVLR GNLFFKTVEI EQPVYDVKTR EYKHKNAFIV FS HGDLIIK RIRKIAESLD ANLYDVDSSN EGRSQQLAKV NKNLSDLYTV LKTTSTTLES ELYAIAKELD SWFQDVTREK AIF EILNKS NYDTNRKILI AEGWIPRDEL ATLQARLGEM IARLGIDVPS IIQVLDTNHT PPTFHRTNKF TAGFQSICDC YGIA QYREI NAGLPTIVTF PFMFAIMFGD MGHGFLMTLA ALSLVLNEKK INKMKRGEIF DMAFTGRYII LLMGVFSMYT GFLYN DIFS KTMTIFKSGW KWPDHWKKGE SITATSVGTY PIGLDWAWHG TENALLFSNS YKMKLSILMG FIHMTYSYFF SLANHL YFN SMIDIIGNFI PGLLFMQGIF GYLSVCIVYK WAVDWVKDGK PAPGLLNMLI NMFLSPGTID DELYPHQAKV QVFLLLM AL VCIPWLLLVK PLHFKFTHKK KSHEPLPSTE ADASSEDLEA QQLISAMDAD DAEEEEVGSG SHGEDFGDIM IHQVIHTI E FCLNCVSHTA SYLRLWALSL AHAQLSSVLW TMTIQIAFGF RGFVGVFMTV ALFAMWFALT CAVLVLMEGT SAMLHSLRL HWVESMSKFF VGEGLPYEPF AFEYKDMEVA VASASSSASS

UniProtKB: V-type proton ATPase subunit a, vacuolar isoform

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Macromolecule #10: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 39.822484 KDa
SequenceString: MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT ...String:
MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT AEELDDMNIE IIRNKLYKAY LEDFYNFVTE EIPEPAKECM QTLLGFEADR RSINIALNSL QSSDIDPDLK SD LLPNIGK LYPLATFHLA QAQDFEGVRA ALANVYEYRG FLETGNLEDH FYQLEMELCR DAFTQQFAIS TVWAWMKSKE QEV RNITWI AECIAQNQRE RINNYISVY

UniProtKB: V-type proton ATPase subunit d

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Macromolecule #11: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 22.610641 KDa
SequenceString: MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA ...String:
MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA TAAISDAADS ALFVKILVIE IFGSILGLLG LIVGLLMAGK ASEFQ

UniProtKB: V-type proton ATPase subunit c''

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Macromolecule #12: V-type proton ATPase subunit c'

MacromoleculeName: V-type proton ATPase subunit c' / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 17.046361 KDa
SequenceString:
MSTQLASNIY APLYAPFFGF AGCAAAMVLS CLGAAIGTAK SGIGIAGIGT FKPELIMKSL IPVVMSGILA IYGLVVAVLI AGNLSPTED YTLFNGFMHL SCGLCVGFAC LSSGYAIGMV GDVGVRKYMH QPRLFVGIVL ILIFSEVLGL YGMIVALILN T RGSE

UniProtKB: V-type proton ATPase subunit c'

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Macromolecule #13: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 13 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 16.357501 KDa
SequenceString:
MTELCPVYAP FFGAIGCASA IIFTSLGAAY GTAKSGVGIC ATCVLRPDLL FKNIVPVIMA GIIAIYGLVV SVLVCYSLGQ KQALYTGFI QLGAGLSVGL SGLAAGFAIG IVGDAGVRGS SQQPRLFVGM ILILIFAEVL GLYGLIVALL LNSRATQDVV C

UniProtKB: V-type proton ATPase subunit c

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Macromolecule #14: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 8.387065 KDa
SequenceString:
MSSFYTVVGV FIVVSAMSVL FWIMAPKNNQ AVWRSTVILT LAMMFLMWAI TFLCQLHPLV APRRSDLRPE FAE

UniProtKB: V-type proton ATPase subunit e

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Macromolecule #15: V0 assembly protein 1

MacromoleculeName: V0 assembly protein 1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 29.694885 KDa
SequenceString: MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK ...String:
MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK SGDNLTVVIN SLGWAFEDED GDDEYATEET LSHHDNNKGK EGDDDILSSI WTEGLLMCLI VSALLLFILI VA LSWISNL DITYGALEKS TNPIKKNN

UniProtKB: V0 assembly protein 1

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Macromolecule #16: Yeast Vacuolar ATPase f subunit

MacromoleculeName: Yeast Vacuolar ATPase f subunit / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 9.369934 KDa
SequenceString:
MRPVVSTGKA WCCTVLSAFG VVILSVIAHL FNTNHESFVG SINDPEDGPA VAHTVYLAAL VYLVFFVFCG FQVYLARRKP SIELR

UniProtKB: V-type proton ATPase subunit f

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 85109 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 85109
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7fda:
CryoEM Structure of Reconstituted V-ATPase, state1

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