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- EMDB-31541: CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 -

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Basic information

Entry
Database: EMDB / ID: EMD-31541
TitleCryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1
Map data
Sample
  • Complex: Oxr1 bound V1 subcomplex of Yeast Vacuolar ATPase
    • Complex: Yeast Vacuolar ATPase subunit C
      • Protein or peptide: V-type proton ATPase subunit C
    • Complex: Yeast V-type proton ATPase subunits
      • Protein or peptide: V-type proton ATPase subunit E
      • Protein or peptide: V-type proton ATPase subunit G
      • 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 D
      • Protein or peptide: V-type proton ATPase subunit F
      • Protein or peptide: Oxidation resistance protein 1
KeywordsATPase / proton pump / rotary motor enzyme / membrane protein / MOTOR PROTEIN
Function / homology
Function and homology information


vacuole-mitochondrion membrane contact site / protein retention in Golgi apparatus / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / protein-containing complex disassembly / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / pexophagy ...vacuole-mitochondrion membrane contact site / protein retention in Golgi apparatus / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / protein-containing complex disassembly / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / pexophagy / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / ATP metabolic process / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / transmembrane transport / intracellular calcium ion homeostasis / cytoplasmic stress granule / response to oxidative stress / membrane raft / Golgi membrane / mitochondrion / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
TLDc domain / TLD / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / V-type ATPase subunit E ...TLDc domain / TLD / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit C / V-type proton ATPase subunit D / V-type proton ATPase subunit F / Oxidation resistance protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 29, 2021-
Map releaseDec 29, 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: 0.7
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
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  • Surface view with fitted model
  • Atomic models: PDB-7fde
  • Surface level: 0.7
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31541.png

Downloads & links

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Map

FileDownload / File: emd_31541.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-1.172409 - 3.3534698
Average (Standard dev.)0.0012109595 (±0.12922302)
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-1.1723.3530.001

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Supplemental data

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Sample components

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Entire : Oxr1 bound V1 subcomplex of Yeast Vacuolar ATPase

EntireName: Oxr1 bound V1 subcomplex of Yeast Vacuolar ATPase
Components
  • Complex: Oxr1 bound V1 subcomplex of Yeast Vacuolar ATPase
    • Complex: Yeast Vacuolar ATPase subunit C
      • Protein or peptide: V-type proton ATPase subunit C
    • Complex: Yeast V-type proton ATPase subunits
      • Protein or peptide: V-type proton ATPase subunit E
      • Protein or peptide: V-type proton ATPase subunit G
      • 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 D
      • Protein or peptide: V-type proton ATPase subunit F
      • Protein or peptide: Oxidation resistance protein 1

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Supramolecule #1: Oxr1 bound V1 subcomplex of Yeast Vacuolar ATPase

SupramoleculeName: Oxr1 bound V1 subcomplex of Yeast Vacuolar ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 600 KDa

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Supramolecule #2: Yeast Vacuolar ATPase subunit C

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

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Supramolecule #3: Yeast V-type proton ATPase subunits

SupramoleculeName: Yeast V-type proton ATPase subunits / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#8 / Details: V-ATPase subunits purified from natural source

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Macromolecule #1: V-type proton ATPase subunit C

MacromoleculeName: V-type proton ATPase subunit C / type: protein_or_peptide / ID: 1 / 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 #2: V-type proton ATPase subunit E

MacromoleculeName: V-type proton ATPase subunit E / type: protein_or_peptide / ID: 2 / 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 #3: V-type proton ATPase subunit G

MacromoleculeName: V-type proton ATPase subunit G / type: protein_or_peptide / ID: 3 / 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 #4: Yeast Vacuolar ATPase A subunit

MacromoleculeName: Yeast Vacuolar ATPase A subunit / type: protein_or_peptide / ID: 4 / 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 #5: V-type proton ATPase subunit B

MacromoleculeName: V-type proton ATPase subunit B / type: protein_or_peptide / ID: 5 / 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 #6: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 6 / 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 #7: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 7 / 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 #8: Oxidation resistance protein 1

MacromoleculeName: Oxidation resistance protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 30.818334 KDa
SequenceString: MFGVKDAIFK IKRSIAGTDS SDSTAYTTAS ESSPQLKDSH NPFRNKTTSE RTIVEEGSLP PVRLNGYLPS TKNKLLTPEM CDEIRTLMP TRIQLYTEWN LLYSLEQHGS SLHSLYSNVA PDSKEFRRVG YVLVIKDRKN GIFGAYSNEA FHPNEHRQYT G NGECFLWK ...String:
MFGVKDAIFK IKRSIAGTDS SDSTAYTTAS ESSPQLKDSH NPFRNKTTSE RTIVEEGSLP PVRLNGYLPS TKNKLLTPEM CDEIRTLMP TRIQLYTEWN LLYSLEQHGS SLHSLYSNVA PDSKEFRRVG YVLVIKDRKN GIFGAYSNEA FHPNEHRQYT G NGECFLWK LDKVPDVNIS EKEESEQEGK EGKEEGDKEE RWRFSGYPYT GVNEFAIYCT SEFLSMGAGD GHYGLLCDDG LL HGVSNPC QTYGNEVLSK EGKKFSIVAL EVWRVG

UniProtKB: Oxidation resistance protein 1

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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: 20447 / 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 20447
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7fde:
CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1

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