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- EMDB-6810: V/A-type ATPase/synthase from Thermus thermophilus, rotational state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-6810
TitleV/A-type ATPase/synthase from Thermus thermophilus, rotational state 1
Map dataThe density map of V-type ATP synthase, state 1, from thermophilic bacterium, Thermus thermophilus.
Sample
  • Complex: V/A-type ATPase/synthase from Thermus thermophilus, rotational state 1.
    • 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 D
    • Protein or peptide: V-type ATP synthase subunit F
    • Protein or peptide: V-type ATP synthase, subunit (VAPC-THERM)
    • Protein or peptide: V-type ATP synthase subunit E
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsATP synthase / proton pump / V-ATPase / Bioenergetics / MOTOR PROTEIN
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 / 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 / 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-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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type ATP synthase subunit D / 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 I / V-type ATP synthase, subunit K
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsNakanishi A / Kishikawa J
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Education, Science and Culture of Japan17H03648 Japan
Ministry of Education, Science and Culture of Japan16K21472 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Cryo EM structure of intact rotary H-ATPase/synthase from Thermus thermophilus.
Authors: Atsuko Nakanishi / Jun-Ichi Kishikawa / Masatada Tamakoshi / Kaoru Mitsuoka / Ken Yokoyama /
Abstract: Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor ...Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor complex against the surrounding peripheral stator apparatus. Here, we present a large data set of single particle cryo-electron micrograph images of the V/A type H-rotary ATPase from the bacterium Thermus thermophilus, enabling the identification of three rotational states based on the orientation of the rotor subunit. Using masked refinement and classification with signal subtractions, we obtain homogeneous reconstructions for the whole complexes and soluble V domains. These reconstructions are of higher resolution than any EM map of intact rotary ATPase reported previously, providing a detailed molecular basis for how the rotary ATPase maintains structural integrity of the peripheral stator apparatus, and confirming the existence of a clear proton translocation path from both sides of the membrane.
History
DepositionAug 10, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
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: 0.098
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.098
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5y5x
  • Surface level: 0.098
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6810.png

Downloads & links

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Map

FileDownload / File: emd_6810.map.gz / Format: CCP4 / Size: 50.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe density map of V-type ATP synthase, state 1, from thermophilic bacterium, Thermus thermophilus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 236 pix.
= 330.4 Å		1.4 Å/pix.
x 236 pix.
= 330.4 Å		1.4 Å/pix.
x 236 pix.
= 330.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.098 / Movie #1: 0.098
Minimum - Maximum-0.3401349 - 0.54437363
Average (Standard dev.)0.00053630606 (±0.024898827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions236236236
Spacing236236236
CellA=B=C: 330.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z236236236
origin x/y/z0.0000.0000.000
length x/y/z330.400330.400330.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS236236236
D min/max/mean-0.3400.5440.001

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Supplemental data

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Sample components

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Entire : V/A-type ATPase/synthase from Thermus thermophilus, rotational st...

EntireName: V/A-type ATPase/synthase from Thermus thermophilus, rotational state 1.
Components
  • Complex: V/A-type ATPase/synthase from Thermus thermophilus, rotational state 1.
    • 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 D
    • Protein or peptide: V-type ATP synthase subunit F
    • Protein or peptide: V-type ATP synthase, subunit (VAPC-THERM)
    • Protein or peptide: V-type ATP synthase subunit E
    • Protein or peptide: V-type ATP synthase subunit C
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: V/A-type ATPase/synthase from Thermus thermophilus, rotational st...

SupramoleculeName: V/A-type ATPase/synthase from Thermus thermophilus, rotational state 1.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 650 KDa

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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 HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 63.69998 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 FKALA

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 HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 53.2195 KDa
SequenceString: MDLLKKEYTG ITYISGPLLF VENAKDLAYG AIVDIKDGTG RVRGGQVIEV SEEYAVIQVF EETTGLDLAT TSVSLVEDVA RLGVSKEML GRRFNGIGKP IDGLPPITPE KRLPITGLPL NPVARRKPEQ FIQTGISTID VMNTLVRGQK LPIFSGSGLP A NEIAAQIA ...String:
MDLLKKEYTG ITYISGPLLF VENAKDLAYG AIVDIKDGTG RVRGGQVIEV SEEYAVIQVF EETTGLDLAT TSVSLVEDVA RLGVSKEML GRRFNGIGKP IDGLPPITPE KRLPITGLPL NPVARRKPEQ FIQTGISTID VMNTLVRGQK LPIFSGSGLP A NEIAAQIA RQATVRPDLS GEGEKEEPFA VVFAAMGITQ RELSYFIQEF ERTGALSRSV LFLNKADDPT IERILTPRMA LT VAEYLAF EHDYHVLVIL TDMTNYCEAL REIGAAREEI PGRRGYPGYM YTDLATIYER AGVVEGKKGS VTQIPILSMP DDD RTHPIP DLTGYITEGQ IQLSRELHRK GIYPPIDPLP SLSRLMNNGV GKGKTREDHK QVSDQLYSAY ANGVDIRKLV AIIG EDALT ENDRRYLQFA DAFERFFINQ GQQNRSIEES LQIAWALLSM LPQGELKRIS KDHIGKYYGQ KLEEIWGAPQ ALD

UniProtKB: V-type ATP synthase beta chain

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Macromolecule #3: V-type ATP synthase subunit D

MacromoleculeName: V-type ATP synthase subunit D / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 24.715566 KDa
SequenceString: MSQVSPTRMN LLQRRGQLRL AQKGVDLLKK KRDALVAEFF GLVREAMEAR KALDQAAKEA YAALLLAQAF DGPEVVAGAA LGVPPLEGV EAEVENVWGS KVPRLKATFP DGALLSPVGT PAYTLEASRA FRRYAEALIR VANTETRLKK IGEEIKKTTR R VNALEQVV ...String:
MSQVSPTRMN LLQRRGQLRL AQKGVDLLKK KRDALVAEFF GLVREAMEAR KALDQAAKEA YAALLLAQAF DGPEVVAGAA LGVPPLEGV EAEVENVWGS KVPRLKATFP DGALLSPVGT PAYTLEASRA FRRYAEALIR VANTETRLKK IGEEIKKTTR R VNALEQVV IPGIRAQIRF IQQVLEQRER EDTFRLKRIK GKIEAREAEE EGGRPNPQVE IGAGL

UniProtKB: V-type ATP synthase subunit D

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Macromolecule #4: V-type ATP synthase subunit F

MacromoleculeName: V-type ATP synthase subunit F / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 11.294904 KDa
SequenceString:
MAVIADPETA QGFRLAGLEG YGASSAEEAQ SLLETLVERG GYALVAVDEA LLPDPERAVE RLMRGRDLPV LLPIAGLKEA FQGHDVEGY MRELVRKTIG FDIKL

UniProtKB: V-type ATP synthase subunit F

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Macromolecule #5: V-type ATP synthase, subunit (VAPC-THERM)

MacromoleculeName: V-type ATP synthase, subunit (VAPC-THERM) / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 13.166218 KDa
SequenceString:
MTGGLVLNAI SRAGGAMGGL GLIKSLAEKE KQLLERLEAA KKEAEERVKR AEAEAKALLE EAEAKAKALE AQYRERERAE TEALLARYR ERAEAEAKAV REKAMARLDE AVALVLKEVL P

UniProtKB: V-type ATP synthase, subunit (VAPC-THERM)

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Macromolecule #6: V-type ATP synthase subunit E

MacromoleculeName: V-type ATP synthase subunit E / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 20.699693 KDa
SequenceString:
MSKLEAILSQ EVEAEIQALL QEAEAKAEAV KREAEEKAKA LLQARERALE AQYRAALRRA ESAGELLVAT ARTQARGEVL EEVRRRVRE ALEALPQKPE WPEVVRKLAL EALEALPGAK ALVANPEDLP HLEAMARERG VELQAEPALR LGVRAVGAEG K TQVENSLL ARMDRAWDAM SSKVAQALWG

UniProtKB: V-type ATP synthase subunit E

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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 HB8 (bacteria) / Strain: HB8
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: V-type ATP synthase subunit I

MacromoleculeName: V-type ATP synthase subunit I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 72.204289 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 HEAYAGGVAA LVVVHRKEVD QAKAALSRAG VAELRLPGAL GELPLSEAAR RLKERAEAAP RELSEVRQHL AK LARESAS TLQSLWTRAQ DEVARLKALE ELASGRFGFA LLGYVPVKAK PKVEEALARH KESVVYAFEP VDEHHEADRI PVV LDNPPW AKPFELLVSF LNTPKYGTFD PTPVVPVFFP FWFGMIVGDI GYALLFYLVG RWLSGYVKRN EPLVIDLFAL KLKP QVIGK LVHILNWMVF WTVVWGVIYG EFFGTFLEHL GVFGTPEHPG LIPILIHRID TAKTANLLIL LSVAFGVVLV FFGLA LRAY LGLKHRHMAH FWEGVGYLGG LVGVLALAAS YLGNLQAGWL QGLMYLGFGV FLLAVLMSRI WLMIPEIFTQ AGHILS HIR IYAVGAAGGI LAGLLTDVGF ALAERLGLLG VLLGLLVAGV LHLLILLLTT LGHMLQPIRL LWVEFFTKFG FYEENGR PY RPFKSVREAQ

UniProtKB: V-type ATP synthase subunit I

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Macromolecule #9: V-type ATP synthase, subunit K

MacromoleculeName: V-type ATP synthase, subunit K / type: protein_or_peptide / ID: 9 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightTheoretical: 9.841714 KDa
SequenceString:
MKKLLVTVLL AVFGALAFAA EEAAASGGLD RGLIAVGMGL AVGLAALGTG VAQARIGAAG VGAIAEDRSN FGTALIFLLL PETLVIFGL LIAFILNGRL

UniProtKB: V-type ATP synthase, subunit K

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration0.027 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris-HCl
0.1 mMEDTA
0.003 %LMNG
GridModel: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 26.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b) / Number images used: 117938
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1b)
Final 3D classificationSoftware - Name: RELION (ver. 2.1b)
FSC plot (resolution estimation)

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