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- EMDB-30034: 2.7A Yeast Vo state3 -

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Basic information

Entry
Database: EMDB / ID: EMD-30034
Title2.7A Yeast Vo state3
Map datasharpen
Sample
  • Complex: V-type proton ATPase Vo sub-complex
    • Protein or peptide: x 8 types
  • Ligand: x 4 types
KeywordsV-ATPase / Vo sub-complex / CryoEM / TRANSPORT PROTEIN
Function / homology
Function and homology information


cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification ...cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / vacuolar transport / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 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 / cellular hyperosmotic response / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / endoplasmic reticulum membrane / membrane
Similarity search - Function
Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 ...Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type proton ATPase subunit f / 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 c' / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsRoh SH / Shekhar M
Funding support United States, Korea, Republic Of, France, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM058600 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD021600 United States
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063865 Korea, Republic Of
National Science Foundation (NSF, United States)MCB-1942763 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM067887 United States
Agence Nationale de la Recherche (ANR)ProteaseInAction Grant France
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V complex.
Authors: Soung-Hun Roh / Mrinal Shekhar / Grigore Pintilie / Christophe Chipot / Stephan Wilkens / Abhishek Singharoy / Wah Chiu /
Abstract: Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, ...Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo-electron microscopy (cryo-EM) structure of yeast V proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V that shows the -ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with -ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.
History
DepositionFeb 22, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m0r
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30034.png

Downloads & links

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Map

FileDownload / File: emd_30034.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.03
Minimum - Maximum-0.13741274 - 0.23216903
Average (Standard dev.)0.00077562843 (±0.010258893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
start NX/NY/NZ107107101
NX/NY/NZ267267267
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1370.2320.001

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Supplemental data

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Additional map: unfil

Fileemd_30034_additional_1.map
Annotationunfil
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : V-type proton ATPase Vo sub-complex

EntireName: V-type proton ATPase Vo sub-complex
Components
  • Complex: V-type proton ATPase Vo sub-complex
    • Protein or peptide: V-type proton ATPase subunit c'
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V0 assembly protein 1
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: Uncharacterized protein YPR170W-B
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit a, vacuolar isoform
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: PYROPHOSPHATE
  • Ligand: (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene
  • Ligand: water

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Supramolecule #1: V-type proton ATPase Vo sub-complex

SupramoleculeName: V-type proton ATPase Vo sub-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 400 kDa/nm

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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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.414615 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
SNIYAPLYAP FFGFAGCAAA MVLSCLGAAI GTAKSGIGIA GIGTFKPELI MKSLIPVVMS GILAIYGLVV AVLIAGNLSP TEDYTLFNG FMHLSCGLCV GFACLSSGYA IGMVGDVGVR KYMHQPRLFV GIVLILIFSE VLGLYGMIVA LILNTRGSE

UniProtKB: V-type proton ATPase subunit c'

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Macromolecule #2: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 20.880686 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: SFSHFLYYLV LIVVIVYGLY KLFTGHGSDI NFGKFLLRTS PYMWANLGIA LCVGLSVVGA AWGIFITGSS MIGAGVRAPR ITTKNLISI IFCEVVAIYG LIIAIVFSSK LTVATAENMY SKSNLYTGYS LFWAGITVGA SNLICGIAVG ITGATAAISD A ADSALFVK ...String:
SFSHFLYYLV LIVVIVYGLY KLFTGHGSDI NFGKFLLRTS PYMWANLGIA LCVGLSVVGA AWGIFITGSS MIGAGVRAPR ITTKNLISI IFCEVVAIYG LIIAIVFSSK LTVATAENMY SKSNLYTGYS LFWAGITVGA SNLICGIAVG ITGATAAISD A ADSALFVK ILVIEIFGSI LGLLGLIVGL LMAGKASEFQ

UniProtKB: V-type proton ATPase subunit c''

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Macromolecule #3: V0 assembly protein 1

MacromoleculeName: V0 assembly protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 5.752846 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
DDILSSIWTE GLLMCLIVSA LLLFILIVAL SWISNLDITY GALEKSTNPI KK

UniProtKB: V0 assembly protein 1

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Macromolecule #4: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.186875 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSSFYTVVGV FIVVSAMSVL FWIMAPKNNQ AVWRSTVILT LAMMFLMWAI TFLCQLHPLV APRRSDLRPE F

UniProtKB: V-type proton ATPase subunit e

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Macromolecule #5: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 5 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.254358 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MTELCPVYAP FFGAIGCASA IIFTSLGAAY GTAKSGVGIC ATCVLRPDLL FKNIVPVIMA GIIAIYGLVV SVLVCYSLGQ KQALYTGFI QLGAGLSVGL SGLAAGFAIG IVGDAGVRGS SQQPRLFVGM ILILIFAEVL GLYGLIVALL LNSRATQDVV

UniProtKB: V-type proton ATPase subunit c

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Macromolecule #6: Uncharacterized protein YPR170W-B

MacromoleculeName: Uncharacterized protein YPR170W-B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.487627 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
TGKAWCCTVL SAFGVVILSV IAHLFNTNHE SFVGSINDPE DGPAVAHTVY LAALVYLVFF VFCGFQVYL

UniProtKB: V-type proton ATPase subunit f

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Macromolecule #7: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.822484 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 #8: V-type proton ATPase subunit a, vacuolar isoform

MacromoleculeName: V-type proton ATPase subunit a, vacuolar isoform / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 94.289039 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: EKEEAIFRSA EMALVQFYIP QEISRDSAYT LGQLGLVQFR DLNSKVRAFQ RTFVNEIRRL DNVERQYRYF YSLLKKHDIK LYEGDTDKY LDGSGELYVP PSGSVIDDYV RNASYLEERL IQMEDATDQI EVQKNDLEQY RFILQSGDEF FLKGDNTDST S YMDEDMID ...String:
EKEEAIFRSA EMALVQFYIP QEISRDSAYT LGQLGLVQFR DLNSKVRAFQ RTFVNEIRRL DNVERQYRYF YSLLKKHDIK LYEGDTDKY LDGSGELYVP PSGSVIDDYV RNASYLEERL IQMEDATDQI EVQKNDLEQY RFILQSGDEF FLKGDNTDST S YMDEDMID ANGENIAAAI GASVNYVTGV IARDKVATLE QILWRVLRGN LFFKTVEIEQ PVYDVKTREY KHKNAFIVFS HG DLIIKRI RKIAESLDAN LYDVDSSNEG RSQQLAKVNK NLSDLYTVLK TTSTTLESEL YAIAKELDSW FQDVTREKAI FEI LNKSNY DTNRKILIAE GWIPRDELAT LQARLGEMIA RLGIDVPSII QVLDTNHTPP TFHRTNKFTA GFQSICDCYG IAQY REINA GLPTIVTFPF MFAIMFGDMG HGFLMTLAAL SLVLNEKKIN KMKRGEIFDM AFTGRYIILL MGVFSMYTGF LYNDI FSKT MTIFKSGWKW PDHWKKGESI TATSVGTYPI GLDWAWHGTE NALLFSNSYK MKLSILMGFI HMTYSYFFSL ANHLYF NSM IDIIGNFIPG LLFMQGIFGY LSVCIVYKWA VDWVKDGKPA PGLLNMLINM FLSPGTIDDE LYPHQAKVQV FLLLMAL VC IPWLLLVKPL HFKFTHKKKS HEPLPSTEAD ASSEDLEAQQ LISAMDADDA EEEEVGSGSH GEDFGDIMIH QVIHTIEF C LNCVSHTASY LRLWALSLAH AQLSSVLWTM TIQIAFGFRG FVGVFMTVAL FAMWFALTCA VLVLMEGTSA MLHSLRLHW VESMSKFFVG EGLPYEPFAF EYKDM

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

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Macromolecule #10: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 10 / Number of copies: 30 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #11: PYROPHOSPHATE

MacromoleculeName: PYROPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: PPV
Molecular weightTheoretical: 177.975 Da
Chemical component information

ChemComp-PPV:
PYROPHOSPHATE

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Macromolecule #12: (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22...

MacromoleculeName: (6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene
type: ligand / ID: 12 / Number of copies: 1 / Formula: EYR
Molecular weightTheoretical: 548.968 Da
Chemical component information

ChemComp-EYR:
(6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 184 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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