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- EMDB-12210: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -

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Basic information

Entry
Database: EMDB / ID: EMD-12210
TitleFormate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, composite structure)
Map dataComposite map of the heterodislfide reductase core and mobile arm in state 1 of the formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from M. hungatei
Sample
  • Complex: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
    • Protein or peptide: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
    • Protein or peptide: CoB--CoM heterodisulfide reductase subunit CCoB—CoM heterodisulfide reductase
    • Protein or peptide: CoB--CoM heterodisulfide reductase subunit BCoB—CoM heterodisulfide reductase
    • Protein or peptide: F420-non-reducing hydrogenase subunit D
    • Protein or peptide: Formate dehydrogenase, beta subunit (F420)
    • Protein or peptide: Formate dehydrogenase
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / formate metabolic process / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / FAD dependent oxidoreductase / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal ...F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / FAD dependent oxidoreductase / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / 4Fe-4S dicluster domain / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
F420-non-reducing hydrogenase subunit D / CoB--CoM heterodisulfide reductase iron-sulfur subunit A / CoB--CoM heterodisulfide reductase subunit B / CoB--CoM heterodisulfide reductase subunit C / Formate dehydrogenase, beta subunit (F420) / Formate dehydrogenase, alpha subunit (F420)
Similarity search - Component
Biological speciesMethanospirillum hungatei JF-1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPfeil-Gardiner O / Watanabe T / Shima S / Murphy BJ
Funding support Germany, Japan, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SH 87/1-1 Germany
Japan Society for the Promotion of Science (JSPS) Japan
Alexander von Humboldt Foundation Germany
CitationJournal: Science / Year: 2021
Title: Three-megadalton complex of methanogenic electron-bifurcating and CO-fixing enzymes.
Authors: Tomohiro Watanabe / Olivia Pfeil-Gardiner / Jörg Kahnt / Jürgen Koch / Seigo Shima / Bonnie J Murphy /
Abstract: The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly ...The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly reducing electrons for this reaction are generated by heterodisulfide reductase (Hdr) in complex with hydrogenase or formate dehydrogenase (Fdh) using a flavin-based electron-bifurcation mechanism. Here, we report enzymological and structural characterizations of Fdh-Hdr-Fmd complexes from . The complexes catalyze this reaction using electrons from formate and the reduced form of the electron carrier F. Conformational changes in HdrA mediate electron bifurcation, and polyferredoxin FmdF directly transfers electrons to the CO reduction site, as evidenced by methanofuran-dependent flavin-based electron bifurcation even without free ferredoxin, a diffusible electron carrier between Hdr and Fmd. Conservation of Hdr and Fmd structures suggests that this complex is common among hydrogenotrophic methanogens.
History
DepositionJan 15, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bkd
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bkd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12210.png

Downloads & links

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Map

FileDownload / File: emd_12210.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the heterodislfide reductase core and mobile arm in state 1 of the formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from M. hungatei
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-70.13919 - 101.01617
Average (Standard dev.)0.0053302553 (±1.1846588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 361.584 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z361.584361.584361.584
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ432432432
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-70.139101.0160.005

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Supplemental data

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Sample components

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Entire : Dimeric formate dehydrogenase - heterodisulfide reductase - formy...

EntireName: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
Components
  • Complex: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
    • Protein or peptide: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
    • Protein or peptide: CoB--CoM heterodisulfide reductase subunit CCoB—CoM heterodisulfide reductase
    • Protein or peptide: CoB--CoM heterodisulfide reductase subunit BCoB—CoM heterodisulfide reductase
    • Protein or peptide: F420-non-reducing hydrogenase subunit D
    • Protein or peptide: Formate dehydrogenase, beta subunit (F420)
    • Protein or peptide: Formate dehydrogenase
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Dimeric formate dehydrogenase - heterodisulfide reductase - formy...

SupramoleculeName: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea) / Location in cell: cytoplasm
Molecular weightTheoretical: 948 KDa

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Macromolecule #1: CoB--CoM heterodisulfide reductase iron-sulfur subunit A

MacromoleculeName: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on a sulfur group of donors
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 72.885062 KDa
SequenceString: MAENTEPRIG VFVCHCGTNI AGSMSIDDVV NYAKTLPYVA VADQYQYMCS TPGQKKIDDA IKEYNLTGVV VAACSPRLHE PTFRTATKE GGLNPFRFEM ANIREQNSWV HMHGMWDEAT QKAKDQVRMA VAKAAKLEDL VPKSVPVEKT AMVVGGGVAG M QAALDLAS ...String:
MAENTEPRIG VFVCHCGTNI AGSMSIDDVV NYAKTLPYVA VADQYQYMCS TPGQKKIDDA IKEYNLTGVV VAACSPRLHE PTFRTATKE GGLNPFRFEM ANIREQNSWV HMHGMWDEAT QKAKDQVRMA VAKAAKLEDL VPKSVPVEKT AMVVGGGVAG M QAALDLAS AGIKTYLIER TPTIGGRMSQ LDKTFPTLDC SQCILTPKMV DVGRHPNIEM MTYTEVEKVE GYIGNFDVTL RK KARGVLT PTEATAKGIV GGGCNGCGDC SAVCPVIKPN PFEMGMAPRK AIYIYHAQVM PLIYTVDFDS CVKCGLCVEA CGD KKAIDL EMQDEFITVK VGTAVLATGY ELFPIENKRE WGYKQFDNVI NALEFERLIC ASGPTGGHLV RPSDGKTPMK VGFV LCAGS RDNTGIGKPY CSRFCCMYSL KHAHQIMEKI PGAVAYLFYM DIRSFGKMYE EFYYRIQHEG AKFIRGRVAN VLEDK ETKN LHVFTEDTLL GRPVDVEVDL LVLAAAVQPN EGANELRKKF GVSASQDGWM LEAHPKLNPC GTTTAGVFLA GVCQGP KDI PDTVAQAEGA ASAASIPIHM GEVELEPYFA MCIDELCAGC GMCVNLCPYS ALSLGEKNGR TVMVVTEAKC KGCGTCG GF CPGGAIKMQH FTTPQIVAQI DAFFAGGEQ

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Macromolecule #2: CoB--CoM heterodisulfide reductase subunit C

MacromoleculeName: CoB--CoM heterodisulfide reductase subunit C / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 21.706963 KDa
SequenceString:
MAAKSYNIPE LDKKLADRRY HLSDTNPEFT QKILKTSRTI ANMCYQCGTC TGSCPSAPRS SYRIRLFMRR CVLGLENEAL TDPDLWLCT TCYSCTDRCP RDIAPTDVIM AMRNLAFKRD IVPKNFLQTV QLIYNSGHGV PNNDVNRAAR TKLGLPADPP T THSYPEFV KGIQKIIDHY ELKENADRIL KGD

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Macromolecule #3: CoB--CoM heterodisulfide reductase subunit B

MacromoleculeName: CoB--CoM heterodisulfide reductase subunit B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 32.930938 KDa
SequenceString: MHEYAFFLGC IAPNRYPGCE ASAIKTSEKV GIKLLPLKGA SCCPAPGAFG SIDLNVWYAM AARNLVLAEE MKKDIALICN GCYKSIWEV NHILKHNDEL RDNVNEVLAE IDMQFKGTID VWHLAELYYD DKVCGVQKIK DSVTTPLSGA KVAAHYGCHL M KPKKERHF ...String:
MHEYAFFLGC IAPNRYPGCE ASAIKTSEKV GIKLLPLKGA SCCPAPGAFG SIDLNVWYAM AARNLVLAEE MKKDIALICN GCYKSIWEV NHILKHNDEL RDNVNEVLAE IDMQFKGTID VWHLAELYYD DKVCGVQKIK DSVTTPLSGA KVAAHYGCHL M KPKKERHF GDTENPMWFE ELIGALGAEP IQYRNKMQCC GAGGGVRGYD IVHALDITNE KLINIQEAGA DAITELCPFC QL QFDRGQI EIKEKFGDVY NIPVLHYNEL LGLAQGMSPQ DLALDLHAID CTPFLQKVL

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Macromolecule #4: F420-non-reducing hydrogenase subunit D

MacromoleculeName: F420-non-reducing hydrogenase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 15.692425 KDa
SequenceString:
MADDWKPQIL AIICNWCSYA GADLAGGARI QYPPTVRAIR VMCTGRVDML FILKAFVEGA DGVLVSGCHF GDCHYLEGNY KAAKRMFMI KNLLRNIGLD DRRFRMTFVS ASEGAKWGMV MEDVTNTIKE LGPSPIKEFK K

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Macromolecule #5: Formate dehydrogenase, beta subunit (F420)

MacromoleculeName: Formate dehydrogenase, beta subunit (F420) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 45.639895 KDa
SequenceString: MAAKGDMLYA WAKDAEIQKK GECGGAVTAL LKHALETKMV DAVVAIKKGK DLYDAVPTVI TNPEDIIQTA GSLHCGTLLI PKLIKKYLN GAKDMKLAVT CKGCDAMAFY ELAKRNQINL DNIIMIGVNC GGSVSPVTAR KMISNKFGVD PDTVHKEEID K GQFIIEYE ...String:
MAAKGDMLYA WAKDAEIQKK GECGGAVTAL LKHALETKMV DAVVAIKKGK DLYDAVPTVI TNPEDIIQTA GSLHCGTLLI PKLIKKYLN GAKDMKLAVT CKGCDAMAFY ELAKRNQINL DNIIMIGVNC GGSVSPVTAR KMISNKFGVD PDTVHKEEID K GQFIIEYE GGHKGIKIDE LEEEGYGRRS NCRRCKMKIP RQADIAAGNW GVIGDKAGKA TFLEICSEKG ANLVNSAQSK GA LEISPAD PKGIDIRAKV EKAMFNLGDE WRHRDFEGMG KGKDRLKLMM SESSKCIKCY ACVEACPICY CIECSTKKPW YIA PGVLPT SFMFHLIRFA HVSDSCINCG QCEELCPMEI PNALFMHSQQ VEIEKMFGHI PGQDMTPPIH AFVEEKAERA RLDA TGTDS IYTNIFTDE

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Macromolecule #6: Formate dehydrogenase

MacromoleculeName: Formate dehydrogenase / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)
Molecular weightTheoretical: 75.911445 KDa
SequenceString: MSENSEIMKY VATTCPYCGV GCTLNLVVSN GKVVGVEPNQ RSPINEGKLC PKGVTCWEHI HSPDRLTTPL IKKDGKFIEA SWDEALDLV AKNLKVIYDK HGPKGLGFQT SCRTVNEDCY IFQKFARVGF KTNNVDNCAR ICHGPSVAGL SLSFGSGAAT N GFEDALNA ...String:
MSENSEIMKY VATTCPYCGV GCTLNLVVSN GKVVGVEPNQ RSPINEGKLC PKGVTCWEHI HSPDRLTTPL IKKDGKFIEA SWDEALDLV AKNLKVIYDK HGPKGLGFQT SCRTVNEDCY IFQKFARVGF KTNNVDNCAR ICHGPSVAGL SLSFGSGAAT N GFEDALNA DLILIWGSNA VEAHPLAGRR IAQAKKKGIQ IIAVDPRYTM TARLADTYVR FNPSTHIALA NSMMYWIIKE GL EDKKFIQ DRVNGFEDLK KTVENYADAE AIHGVPLDVV KDIAFRYAKA KNAVIIYCLG ITELTTGTDN VRSMGNLALL TGN VGREGV GVNPLRGQNN VQGACDMGAY PNVYSGYQKC EVAENRAKME KAWSVTNLPD WYGATLTEQI NQCGDEIKGM YILG LNPVV TYPSSNHVKA QLEKLDFLVV QDIFFTETCQ YADVILPGAC FAEKDGTFTS GERRINRVRK AVNPPGQAKE DIHII SELA AKMGFKGFEL PTAKDVWDDM RAVTPSMFGA TYEKLERPEG ICWPCPTEEH PGTPILHREK FATADGKGNL FGIDYR PPA EVADAEYPFT LMTGRLIFHY HSRTQTDRAA DLHREVPESY AQINIEDARR LGIKNNEYIK LKSRRGETTT LARVTDE VA PGVVYMTMHF ADGVNNLTNT VLDPMSKMPE LKHCAISIEK VGGN

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 18 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

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Macromolecule #8: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 3 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM / Flavin adenine dinucleotide

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Macromolecule #9: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 9 / Number of copies: 4 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

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Macromolecule #10: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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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

Concentration0.5 mg/mL
BufferpH: 7.6 / Component - Concentration: 25.0 mM / Component - Formula: Tris-HClTris / Component - Name: Tris-HClTris
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER
DetailsPreparation in an anaerobic tent (O2 < 20 ppm at all times, nearly always < 2ppm)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8745 / Average electron dose: 50.0 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), RELION (ver. 3.1))
Startup modelType of model: OTHER
Details: ab initio model generation, stochastic gradient descent, Relion 3
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 300000 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: This applies to the map of the mobile arm in state1. The uploaded map is a composite map.
Number images used: 277450
DetailsRecorded in counted mode

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7bkd:
Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, composite structure)

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