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- EMDB-8017: Thermus thermophilus V/A-ATPase, conformation 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-8017
TitleThermus thermophilus V/A-ATPase, conformation 2
Map dataNone
Sample
  • Complex: Intact Thermus thermophilus V/A-ATPase
    • Protein or peptide: V-type ATP synthase alpha chain
    • Protein or peptide: V-type ATP synthase beta chain
    • Protein or peptide: V-type ATP synthase subunit E
    • Protein or peptide: V-type ATPase subunit GV-ATPase
    • Protein or peptide: V-type ATP synthase subunit D
    • Protein or peptide: V-type ATP synthase subunit F
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: Archaeal/vacuolar-type H+-ATPase subunit I
    • Protein or peptide: Vacuolar type ATP synthase subunit
KeywordsV/A-ATPase / V-ATPase / A-ATPase / Thermus thermophilus / rotary ATPase / membrane protein / HYDROLASE
Function / homology
Function and homology information


proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / metal ion binding
Similarity search - Function
V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d ...V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-ATPase proteolipid subunit / 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-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 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type ATP synthase subunit I / V-type ATP synthase subunit D / F0F1 ATP synthase subunit C / V-type ATP synthase subunit E / V-type ATP synthase subunit C / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain / V-type ATP synthase, subunit (VAPC-THERM) / V-type ATP synthase, subunit K ...V-type ATP synthase subunit I / V-type ATP synthase subunit D / F0F1 ATP synthase subunit C / V-type ATP synthase subunit E / V-type ATP synthase subunit C / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain / V-type ATP synthase, subunit (VAPC-THERM) / V-type ATP synthase, subunit K / V-type ATPase subunit / V-type ATP synthase beta chain / V-type ATP synthase subunit D
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsSchep DG / Zhao J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 81294 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance.
Authors: Daniel G Schep / Jianhua Zhao / John L Rubinstein /
Abstract: Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the ...Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases.
History
DepositionFeb 5, 2016-
Header (metadata) releaseMar 9, 2016-
Map releaseMar 9, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0415
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0415
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gas
  • Surface level: 0.0415
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8017.png

Downloads & links

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Map

FileDownload / File: emd_8017.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.45 Å
Density
Contour LevelBy AUTHOR: 0.0415 / Movie #1: 0.0415
Minimum - Maximum-0.052118573 - 0.11740052
Average (Standard dev.)0.0011404442 (±0.0067767785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0520.1170.001

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Supplemental data

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Sample components

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Entire : Intact Thermus thermophilus V/A-ATPase

EntireName: Intact Thermus thermophilus V/A-ATPase
Components
  • Complex: Intact Thermus thermophilus V/A-ATPase
    • Protein or peptide: V-type ATP synthase alpha chain
    • Protein or peptide: V-type ATP synthase beta chain
    • Protein or peptide: V-type ATP synthase subunit E
    • Protein or peptide: V-type ATPase subunit GV-ATPase
    • Protein or peptide: V-type ATP synthase subunit D
    • Protein or peptide: V-type ATP synthase subunit F
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: Archaeal/vacuolar-type H+-ATPase subunit I
    • Protein or peptide: Vacuolar type ATP synthase subunit

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Supramolecule #1: Intact Thermus thermophilus V/A-ATPase

SupramoleculeName: Intact Thermus thermophilus V/A-ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8

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Macromolecule #1: V-type ATP synthase alpha chain

MacromoleculeName: V-type ATP synthase alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 63.628902 KDa
SequenceString: MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV ...String:
MIQGVIQKIA GPAVIAKGML GARMYDICKV GEEGLVGEII RLDGDTAFVQ VYEDTSGLKV GEPVVSTGLP LAVELGPGML NGIYDGIQR PLERIREKTG IYITRGVVVH ALDREKKWAW TPMVKPGDEV RGGMVLGTVP EFGFTHKILV PPDVRGRVKE V KPAGEYTV EEPVVVLEDG TELKMYHTWP VRRARPVQRK LDPNTPFLTG MRILDVLFPV AMGGTAAIPG PFGSGKTVTQ QS LAKWSNA DVVVYVGCGE RGNEMTDVLV EFPELTDPKT GGPLMHRTVL IANTSNMPVA AREASIYVGV TIAEYFRDQG FSV ALMADS TSRWAEALRE ISSRLEEMPA EEGYPPYLAA RLAAFYERAG KVITLGGEEG AVTIVGAVSP PGGDMSEPVT QSTL RIVGA FWRLDASLAF RRHFPAINWN GSYSLFTSAL DPWYRENVAE DYPELRDAIS ELLQREAGLQ EIVQLVGPDA LQDAE RLVI EVGRIIREDF LQQNAYHEVD AYCSMKKAYG IMKMILAFYK EAEAAIKRGV SIDEILQLPV LERIGRARYV SEEEFP AYF EEAMKEIQGA FKAL

UniProtKB: V-type ATP synthase alpha chain

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Macromolecule #2: V-type ATP synthase beta chain

MacromoleculeName: V-type ATP synthase beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 50.850738 KDa
SequenceString: EYTGITYISG PLLFVENAKD LAYGAIVDIK DGTGRVRGGQ VIEVSEEYAV IQVFEETTGL DLATTSVSLV EDVARLGVSK EMLGRRFNG IGKPIDGLPP ITPEKRLPIT GLPLNPVARR KPEQFIQTGI STIDVMNTLV RGQKLPIFSG SGLPANEIAA Q IARQATVR ...String:
EYTGITYISG PLLFVENAKD LAYGAIVDIK DGTGRVRGGQ VIEVSEEYAV IQVFEETTGL DLATTSVSLV EDVARLGVSK EMLGRRFNG IGKPIDGLPP ITPEKRLPIT GLPLNPVARR KPEQFIQTGI STIDVMNTLV RGQKLPIFSG SGLPANEIAA Q IARQATVR PDLSGEGEKE EPFAVVFAAM GITQRELSYF IQEFERTGAL SRSVLFLNKA DDPTIERILT PRMALTVAEY LA FEHDYHV LVILTDMTNY CEALREIGAA REEIPGRRGY PGYMYTDLAT IYERAGVVEG KKGSVTQIPI LSMPDDDRTH PIP DLTGYI TEGQIQLSRE LHRKGIYPPI DPLPSLSRLM NNGVGKGKTR EDHKQVSDQL YSAYANGVDI RKLVAIIGED ALTE NDRRY LQFADAFERF FINQGQQNRS IEESLQIAWA LLSMLPQGEL KRISKDHIGK YY

UniProtKB: V-type ATP synthase beta chain

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Macromolecule #3: V-type ATP synthase subunit E

MacromoleculeName: V-type ATP synthase subunit E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 20.481418 KDa
SequenceString:
KLEAILSQEV EAEIQALLQE AEAKAEAVKR EAEEKAKALL QARERALEAQ YRAALRRAES AGELLVATAR TQARGEVLEE VRRRVREAL EALPQKPEWP EVVRKLALEA LEALPGAKAL VANPEDLPHL EAMARERGVE LQAEPALRLG VRAVGAEGKT Q VENSLLAR MDRAWDAMSS KVAQALWG

UniProtKB: V-type ATP synthase subunit E

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Macromolecule #4: V-type ATPase subunit G

MacromoleculeName: V-type ATPase subunit G / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 11.752551 KDa
SequenceString:
GMGGLGLIKS LAEKEKQLLE RLEAAKKEAE ERVKRAEAEA KALLEEAEAK AKALEAQYRE RERAETEALL ARYRERAEAE AKAVREKAM ARLDEAVALV LKEVLP

UniProtKB: V-type ATPase subunit

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Macromolecule #5: V-type ATP synthase subunit D

MacromoleculeName: V-type ATP synthase subunit D / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 23.350973 KDa
SequenceString: SQVSPTRMNL LQRRGQLRLA QKGVDLLKKK RDALVAEFFG LVREAMEARK ALDQAAKEAY AALLLAQAFD GPEVVAGAAL GVPPLEGVE AEVENVWGSK VPRLKATFPD GALLSPVGTP AYTLEASRAF RRYAEALIRV ANTETRLKKI GEEIKKTTRR V NALEQVVI ...String:
SQVSPTRMNL LQRRGQLRLA QKGVDLLKKK RDALVAEFFG LVREAMEARK ALDQAAKEAY AALLLAQAFD GPEVVAGAAL GVPPLEGVE AEVENVWGSK VPRLKATFPD GALLSPVGTP AYTLEASRAF RRYAEALIRV ANTETRLKKI GEEIKKTTRR V NALEQVVI PGIRAQIRFI QQVLEQRERE DTFRLKRIKG KIEAREAEEE GG

UniProtKB: V-type ATP synthase subunit D

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Macromolecule #6: V-type ATP synthase subunit F

MacromoleculeName: V-type ATP synthase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 10.824321 KDa
SequenceString:
MAVIADPETA QGFRLAGLEG YGASSAEEAQ SLLETLVERG GYALVAVDEA LLPDPERAVE RLMRGRDLPV LLPIAGLKEA FQGHDVEGY MRELVRKTIG F

UniProtKB: V-type ATP synthase subunit F

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Macromolecule #7: V-type ATP synthase subunit C

MacromoleculeName: V-type ATP synthase subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 35.96857 KDa
SequenceString: MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL ...String:
MADDFAYLNA RVRVRRGTLL KESFFQEALD LSFADFLRLL SETVYGGELA GQGLPDVDRA VLRTQAKLVG DLPRLVTGEA REAVRLLLL RNDLHNLQAL LRAKATGRPF EEVLLLPGTL REEVWRQAYE AQDPAGMAQV LAVPGHPLAR ALRAVLRETQ D LARVEALL AKRFFEDVAK AAKGLDQPAL RDYLALEVDA ENLRTAFKLQ GSGLAPDAFF LKGGRFVDRV RFARLMEGDY AV LDELSGT PFSGLSGVRD LKALERGLRC VLLKEAKKGV QDPLGVGLVL AYVKEREWEA VRLRLLARRA YFGLPRAQVE EEV VCP

UniProtKB: V-type ATP synthase subunit C

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Macromolecule #8: Archaeal/vacuolar-type H+-ATPase subunit I

MacromoleculeName: Archaeal/vacuolar-type H+-ATPase subunit I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 72.272453 KDa
SequenceString: MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA ...String:
MIAPMEKLVL AGPKGRAKEL LQSLQQAGVV HLETLRPEAL SAYQLSPEER AELRRWEAVS AGAEHTLSLL GLEAEPARPF PEGLEAAEK ALSPIQAHAE GLTRQKQELE EELALAQAYL EPLERLAALA HGLDKSPFLR VIPFLLTEKE LPLVEEALRK A LEDRYLLA HEAYAGGVPA LVVVHRKEVD QAKAALSRAG VAELRLPGAL GELPLSEAAR RLKERAEAAP RELSEVRQHL AK LARESAS TLQSLWTRAQ DEVARLKALE ELASGRFGFA LLGYVPVKAK PKVEEALARH KENVVYAFEP VDEHHEADRI PVV LDNPPW VKPFELLVSF LNTPKYGTFD PTPVVPIFFP FWFGMIVGDI GYALLFYLVG RWLSGYVKRN EPLVIDLFAL KLKP PVLAK LVYILNWMVF WTVVWGLIYG EFFGTFLEHL GVFGTPEHPG LIPILIHRID TAKTANLLIL LSVAFGVVMV FAGLI LRAY LGLKHRHMAH FWEGVGYLGG LLGILALAAS YLGNLQAGWL SALMYLGFGV FLLSVVMSSI WLMIPEIFTQ AGHILS HIR IYAVGAAGGI LAGLLTDVGF AMAERLGLIG VLLGIVVAGV LHLLILLLTT LGHMLQPIRL IWVEFFTKFG FYEENGR PY RPFKSVRETQ

UniProtKB: V-type ATP synthase subunit I

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Macromolecule #9: Vacuolar type ATP synthase subunit

MacromoleculeName: Vacuolar type ATP synthase subunit / type: protein_or_peptide / ID: 9 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: AH8
Molecular weightTheoretical: 9.841714 KDa
SequenceString:
MKKLLVTVLL AVFGALAFAA EEAAASGGLD RGLIAVGMGL AVGLAALGTG VAQARIGAAG VGAIAEDRSN FGTALIFLLL PETLVIFGL LIAFILNGRL

UniProtKB: F0F1 ATP synthase subunit C

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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

Concentration7 mg/mL
BufferpH: 8
GridModel: Homemade nanofabricated / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
Details: Homemade nanofabricated 400 mesh copper/rhodium grid
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
Details: Plunged into liquid ethane/propane (FEI VITROBOT MARK III)..

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated magnification: 34483 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 12 / Average exposure time: 15.0 sec. / Average electron dose: 35.7 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5335


Details: Low-pass filtered to 40 Angstrom resolution
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Details: Individual particle motion correction with alignparts_lmbfgs
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 9721

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