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- EMDB-14429: Structure of the Escherichia coli formate hydrogenlyase complex (... -

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Basic information

Entry
Database: EMDB / ID: EMD-14429
TitleStructure of the Escherichia coli formate hydrogenlyase complex (anaerobic preparation, without formate dehydrogenase H)
Map data
Sample
  • Complex: Escherichia coli formate hydrogenlyase complex without formate dehydrogenase H
    • Protein or peptide: x 6 types
  • Ligand: x 9 types
Function / homology
Function and homology information


formate oxidation / formate dehydrogenase complex / plasma membrane respiratory chain complex I / anaerobic electron transport chain / glucose catabolic process / anaerobic respiration / oxidoreductase activity, acting on NAD(P)H / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / quinone binding ...formate oxidation / formate dehydrogenase complex / plasma membrane respiratory chain complex I / anaerobic electron transport chain / glucose catabolic process / anaerobic respiration / oxidoreductase activity, acting on NAD(P)H / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
4Fe-4S dicluster domain / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit ...4Fe-4S dicluster domain / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Formate hydrogenlyase subunit 2 / Formate hydrogenlyase subunit 3 / Formate hydrogenlyase subunit 4 / Formate hydrogenlyase subunit 5 / Formate hydrogenlyase subunit 6 / Formate hydrogenlyase subunit 7
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSteinhilper R / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli.
Authors: Ralf Steinhilper / Gabriele Höff / Johann Heider / Bonnie J Murphy /
Abstract: The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase ...The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H during fermentation, its reversibility, allowing H-dependent CO reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex.
History
DepositionFeb 23, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14429.png

Downloads & links

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Map

FileDownload / File: emd_14429.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.3 Å		0.83 Å/pix.
x 300 pix.
= 249.3 Å		0.83 Å/pix.
x 300 pix.
= 249.3 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.1045647 - 3.6586828
Average (Standard dev.)0.0041000675 (±0.14484973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.29999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14429_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14429_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14429_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia coli formate hydrogenlyase complex without formate de...

EntireName: Escherichia coli formate hydrogenlyase complex without formate dehydrogenase H
Components
  • Complex: Escherichia coli formate hydrogenlyase complex without formate dehydrogenase H
    • Protein or peptide: Formate hydrogenlyase subunit 3
    • Protein or peptide: Formate hydrogenlyase subunit 5
    • Protein or peptide: Formate hydrogenlyase subunit 2
    • Protein or peptide: Formate hydrogenlyase subunit 7
    • Protein or peptide: Formate hydrogenlyase subunit 6
    • Protein or peptide: Formate hydrogenlyase subunit 4
  • Ligand: CARDIOLIPIN
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: NICKEL (II) ION
  • Ligand: CARBONMONOXIDE-(DICYANO) IRON
  • Ligand: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FE (III) ION
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: water

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Supramolecule #1: Escherichia coli formate hydrogenlyase complex without formate de...

SupramoleculeName: Escherichia coli formate hydrogenlyase complex without formate dehydrogenase H
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Details: Sample was prepared anaerobically
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12

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Macromolecule #1: Formate hydrogenlyase subunit 3

MacromoleculeName: Formate hydrogenlyase subunit 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 64.121742 KDa
SequenceString: MSAISLINSG VAWFVAAAVL AFLFSFQKAL SGWIAGIGGA VGSLYTAAAG FTVLTGAVGV SGALSLVSYD VQISPLNAIW LITLGLCGL FVSLYNIDWH RHAQVKCNGL QINMLMAAAV CAVIASNLGM FVVMAEIMAL CAVFLTSNSK EGKLWFALGR L GTLLLAIA ...String:
MSAISLINSG VAWFVAAAVL AFLFSFQKAL SGWIAGIGGA VGSLYTAAAG FTVLTGAVGV SGALSLVSYD VQISPLNAIW LITLGLCGL FVSLYNIDWH RHAQVKCNGL QINMLMAAAV CAVIASNLGM FVVMAEIMAL CAVFLTSNSK EGKLWFALGR L GTLLLAIA CWLLWQRYGT LDLRLLDMRM QQLPLGSDIW LLGVIGFGLL AGIIPLHGWV PQAHANASAP AAALFSTVVM KI GLLGILT LSLLGGNAPL WWGIALLVLG MITAFVGGLY ALVEHNIQRL LAYHTLENIG IILLGLGAGV TGIALEQPAL IAL GLVGGL YHLLNHSLFK SVLFLGAGSV WFRTGHRDIE KLGGIGKKMP VISIAMLVGL MAMAALPPLN GFAGEWVIYQ SFFK LSNSG AFVARLLGPL LAVGLAITGA LAVMCMAKVY GVTFLGAPRT KEAENATCAP LLMSVSVVAL AICCVIGGVA APWLL PMLS AAVPLPLEPA NTTVSQPMIT LLLIACPLLP FIIMAICKGD RLPSRSRGAA WVCGYDHEKS MVITAHGFAM PVKQAF APV LKLRKWLNPV SLVPGWQCEG SALLFRRMAL VELAVLVVII VSRGA

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Macromolecule #2: Formate hydrogenlyase subunit 5

MacromoleculeName: Formate hydrogenlyase subunit 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 66.589859 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MSEEKLGQHY LAALNEAFPG VVLDHAWQTK DQLTVTVKVN YLPEVVEFLY YKQGGWLSVL FGNDERKLNG HYAVYYVLSM EKGHHHHHH HHHHGSTKCW ITVRVEVDAN KPEYPSVTPR VPAAVWGERE VRDMYGLIPV GLPDERRLVL PDDWPDELYP L RKDSMDYR ...String:
MSEEKLGQHY LAALNEAFPG VVLDHAWQTK DQLTVTVKVN YLPEVVEFLY YKQGGWLSVL FGNDERKLNG HYAVYYVLSM EKGHHHHHH HHHHGSTKCW ITVRVEVDAN KPEYPSVTPR VPAAVWGERE VRDMYGLIPV GLPDERRLVL PDDWPDELYP L RKDSMDYR QRPAPTTDAE TYEFINELGD KKNNVVPIGP LHVTSDEPGH FRLFVDGENI IDADYRLFYV HRGMEKLAET RM GYNEVTF LSDRVCGICG FAHSTAYTTS VENAMGIQVP ERAQMIRAIL LEVERLHSHL LNLGLACHFT GFDSGFMQFF RVR ETSMKM AEILTGARKT YGLNLIGGIR RDLLKDDMIQ TRQLAQQMRR EVQELVDVLL STPNMEQRTV GIGRLDPEIA RDFS NVGPM VRASGHARDT RADHPFVGYG LLPMEVHSEQ GCDVISRLKV RINEVYTALN MIDYGLDNLP GGPLMVEGFT YIPHR FALG FAEAPRGDDI HWSMTGDNQK LYRWRCRAAT YANWPTLRYM LRGNTVSDAP LIIGSLDPCY SCTDRMTVVD VRKKKS KVV PYKELERYSI ERKNSPLK

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Macromolecule #3: Formate hydrogenlyase subunit 2

MacromoleculeName: Formate hydrogenlyase subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 21.899289 KDa
SequenceString: MNRFVIADST LCIGCHTCEA ACSETHRQHG LQSMPRLRVM LNEKESAPQL CHHCEDAPCA VVCPVNAITR VDGAVQLNES LCVSCKLCG IACPFGAIEF SGSRPLDIPA NANTPKAPPA PPAPARVSTL LDWVPGIRAI AVKCDLCSFD EQGPACVRMC P TKALHLVD ...String:
MNRFVIADST LCIGCHTCEA ACSETHRQHG LQSMPRLRVM LNEKESAPQL CHHCEDAPCA VVCPVNAITR VDGAVQLNES LCVSCKLCG IACPFGAIEF SGSRPLDIPA NANTPKAPPA PPAPARVSTL LDWVPGIRAI AVKCDLCSFD EQGPACVRMC P TKALHLVD NTDIARVSKR KRELTFNTDF GDLTLFQQAQ SGEAK

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Macromolecule #4: Formate hydrogenlyase subunit 7

MacromoleculeName: Formate hydrogenlyase subunit 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 28.03317 KDa
SequenceString: MSNLLGPRDA NGIPVPMTVD ESIASMKASL LKKIKRSAYV YRVDCGGCNG CEIEIFATLS PLFDAERFGI KVVPSPRHAD ILLFTGAVT RAMRSPALRA WQSAPDPKIC ISYGACGNSG GIFHDLYCVW GGTDKIVPVD VYIPGCPPTP AATLYGFAMA L GLLEQKIH ...String:
MSNLLGPRDA NGIPVPMTVD ESIASMKASL LKKIKRSAYV YRVDCGGCNG CEIEIFATLS PLFDAERFGI KVVPSPRHAD ILLFTGAVT RAMRSPALRA WQSAPDPKIC ISYGACGNSG GIFHDLYCVW GGTDKIVPVD VYIPGCPPTP AATLYGFAMA L GLLEQKIH ARGPGELDEQ PAEILHGDMV QPLRVKVDRE ARRLAGYRYG RQIADDYLTQ LGQGEEQVAR WLEAENDPRL NE IVSHLNH VVEEARIR

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Macromolecule #5: Formate hydrogenlyase subunit 6

MacromoleculeName: Formate hydrogenlyase subunit 6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 20.336395 KDa
SequenceString:
MFTFIKKVIK TGTATSSYPL EPIAVDKNFR GKPEQNPQQC IGCAACVNAC PSNALTVETD LATGELAWEF NLGHCIFCGR CEEVCPTAA IKLSQEYELA VWKKEDFLQQ SRFALCNCRV CNRPFAVQKE IDYAIALLKH NGDSRAENHR ESFETCPECK R QKCLVPSD RIELTRHMKE AI

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Macromolecule #6: Formate hydrogenlyase subunit 4

MacromoleculeName: Formate hydrogenlyase subunit 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 33.049152 KDa
SequenceString: MSVLYPLIQA LVLFAVAPLL SGITRVARAR LHNRRGPGVL QEYRDIIKLL GRQSVGPDAS GWVFRLTPYV MVGVMLTIAT ALPVVTVGS PLPQLGDLIT LLYLFAIARF FFAISGLDTG SPFTAIGASR EAMLGVLVEP MLLLGLWVAA QVAGSTNISN I TDTVYHWP ...String:
MSVLYPLIQA LVLFAVAPLL SGITRVARAR LHNRRGPGVL QEYRDIIKLL GRQSVGPDAS GWVFRLTPYV MVGVMLTIAT ALPVVTVGS PLPQLGDLIT LLYLFAIARF FFAISGLDTG SPFTAIGASR EAMLGVLVEP MLLLGLWVAA QVAGSTNISN I TDTVYHWP LSQSIPLVLA LCACAFATFI EMGKLPFDLA EAEQELQEGP LSEYSGSGFG VMKWGISLKQ LVVLQMFVGV FI PWGQMET FTAGGLLLAL VIAIVKLVVG VLVIALFENS MARLRLDITP RITWAGFGFA FLAFVSLLAA

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Macromolecule #7: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 7 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #8: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 8 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #9: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION / Nickel

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Macromolecule #10: CARBONMONOXIDE-(DICYANO) IRON

MacromoleculeName: CARBONMONOXIDE-(DICYANO) IRON / type: ligand / ID: 10 / Number of copies: 1 / Formula: FCO
Molecular weightTheoretical: 135.89 Da
Chemical component information

ChemComp-FCO:
CARBONMONOXIDE-(DICYANO) IRON

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Macromolecule #11: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL

MacromoleculeName: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
type: ligand / ID: 11 / Number of copies: 1 / Formula: DR9
Molecular weightTheoretical: 746.991 Da
Chemical component information

ChemComp-DR9:
1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL

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Macromolecule #12: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 12 / Number of copies: 7 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #13: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #14: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 14 / Number of copies: 1 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #15: water

MacromoleculeName: water / type: ligand / ID: 15 / Number of copies: 109 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 300386
FSC plot (resolution estimation)

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