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- EMDB-55451: Composite map of the Hdr-Vhu-Fdh dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-55451
TitleComposite map of the Hdr-Vhu-Fdh dimer
Map data
Sample
  • Complex: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
    • Protein or peptide: x 9 types
  • Ligand: x 7 types
KeywordsMethanogenesis / Super-assembly / Flavin-based electron bifurcation / heterodisulfide-reductase / polyferredoxin / formylmethanofuran dehydrogenase / electron transport / oxidoreductase
Biological speciesMethanococcus maripaludis S2 (archaea) / Methanococcus maripaludis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsPaul S / Schuller JM
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)505997786 Germany
European Research Council (ERC)101075992European Union
CitationJournal: To Be Published
Title: An eight-megadalton super-assembly links the first and the last step in methanogenesis to power CO2 reduction
Authors: Paul S / Schuller JM
History
DepositionOct 22, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55451.png

Downloads & links

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Map

FileDownload / File: emd_55451.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.174
Minimum - Maximum0.0 - 1.805227
Average (Standard dev.)0.0002511063 (±0.008860852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 760.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate deh...

EntireName: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
Components
  • Complex: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
    • Protein or peptide: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
    • Protein or peptide: Heterodisulfide reductase subunit B
    • Protein or peptide: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
    • Protein or peptide: Coenzyme F420-reducing hydrogenase, alpha subunit
    • Protein or peptide: F420-non-reducing hydrogenase small subunit
    • Protein or peptide: F420-non-reducing hydrogenase subunit delta
    • Protein or peptide: F420 non-reducing hydrogenase subunit
    • Protein or peptide: formate dehydrogenase (coenzyme F420)
    • Protein or peptide: formate dehydrogenase (coenzyme F420)
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: TUNGSTEN ION
  • Ligand: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

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Supramolecule #1: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate deh...

SupramoleculeName: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7, #9, #8
Source (natural)Organism: Methanococcus maripaludis S2 (archaea)
Molecular weightTheoretical: 8 MDa

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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: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 71.360758 KDa
SequenceString: MSDPKVGVFV CYCGANINGA VDCEAVKDFA SELDGVAVAA TYPFMCADPG QGLIKDAIKE HGLDRIVVAA CTPKIHEPTF RGCLQDAGI SPYYLEFVNI REHDAFVHMG DVEGATRKAC EMIAGGVERA KKLEDVPQKV VDVDKSCMVI GAGIAGIQSA L DLGDQGFK ...String:
MSDPKVGVFV CYCGANINGA VDCEAVKDFA SELDGVAVAA TYPFMCADPG QGLIKDAIKE HGLDRIVVAA CTPKIHEPTF RGCLQDAGI SPYYLEFVNI REHDAFVHMG DVEGATRKAC EMIAGGVERA KKLEDVPQKV VDVDKSCMVI GAGIAGIQSA L DLGDQGFK VYLVDKDESI GGRMAQLAKT FPTDDCAMUI LAPKMVSAAN HPNIELITFA EIKNIDGYIG NFDVTLEKKP RY VDEDTCT GCGACAAACP IEVPNEFDLG LGTRKAIYVP FPQAVPLLYT IDKEHCIDCG LCAKVCCAEA VRYDQKPQEL NIK VGTIIT ATGYDEFDAT KKEEYGYGVY DNVITTLEVE RMINPAGPTH GHEIRPSDGK APKRTVYIQC VGSRDEKVGN PYCS RVCCM FALKNAQLMK MHDPNAEVYI CYMDIRAFGK GYEEYYKRAQ DQFGVKFIRG RPANIFEDPE TKNLTVRVED TLMGE ILEI DADLVVLSAG LEAKKDAGEL AKMLGIDRGP EGFFKELHPK LAPVNTKVDG IAIAGVAQGP KDIPDTVAQA KGAASA VAI PMSQGQFKIE MIRATVNEEV CGGCKVCALM CPYNAITYEE KDGHLVAITD DVACKGCGAC AAACPSGAMQ LRYYRDE QV IGMIDGILNA AKMLEE

UniProtKB: UNIPROTKB: A0A2L1CB19

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Macromolecule #2: Heterodisulfide reductase subunit B

MacromoleculeName: Heterodisulfide reductase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: dihydromethanophenazine:CoB-CoM heterodisulfide reductase
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 32.062203 KDa
SequenceString: MKYAFFLGCI MPNRYAGVES ATRTVMEKLG VELVDMPGAS CCPAPGVFGS FDQKTWLTLA ARNLVIAEEM GTDIVTVCNG CYGSLYEAA HMLHENKEAL AMVNEQLKEI GKEYKGTVHV RHFAELIYKE IGVDKIRENV VKPLAVNIGV HYGCHFLKPT A AKGLGNAE ...String:
MKYAFFLGCI MPNRYAGVES ATRTVMEKLG VELVDMPGAS CCPAPGVFGS FDQKTWLTLA ARNLVIAEEM GTDIVTVCNG CYGSLYEAA HMLHENKEAL AMVNEQLKEI GKEYKGTVHV RHFAELIYKE IGVDKIRENV VKPLAVNIGV HYGCHFLKPT A AKGLGNAE HPTMLDELVE ATGAKSVDYK DKMMCCGAGG GVRAKELDLA LSMTQEKIEN MLAVGADATV NVCPFCQLQF DR GQVEIKE KLGNEYNFPV VHLSQLLGLA MGMDPKEVAL DVNFISPEPL LQKLGY

UniProtKB: UNIPROTKB: A0A7J9NT94

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Macromolecule #3: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2

MacromoleculeName: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 20.48385 KDa
SequenceString:
MMKAEELNKG FVNEIIEAGT PVPGEKEVAS LKSCYQCGTC TGSCPSGRRT AYRTRKVIRQ ALLGIDSVLD SDDIWKCTTC YTCYERCPR DVKVTEIIKT IRNLAAQKGN MAKPHKMTAV YVLKAGHAVP ANDDTAKLRK SIGLAEKAPI AQFSQKDMDE L RTLAKNLK FDELIGFDWK TMGLKQ

UniProtKB: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit C2

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Macromolecule #4: Coenzyme F420-reducing hydrogenase, alpha subunit

MacromoleculeName: Coenzyme F420-reducing hydrogenase, alpha subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: hydrogen dehydrogenase
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 45.687258 KDa
SequenceString: MGKVTIEPLS RLEGHGKVSI TLDDAGKPTD VKLHITALRG FEQFVVGRPA EEVPRIVPRI CGICQTPHHL ASVKAVDAAW GAEVPSAAE KLRELMHLGN MMHSHALHFY YLAAPDFVLG PDSDPAARNI IGVIGAAPEV AKKAIAMRRV GQSIVETIGG R AIHPVTGV ...String:
MGKVTIEPLS RLEGHGKVSI TLDDAGKPTD VKLHITALRG FEQFVVGRPA EEVPRIVPRI CGICQTPHHL ASVKAVDAAW GAEVPSAAE KLRELMHLGN MMHSHALHFY YLAAPDFVLG PDSDPAARNI IGVIGAAPEV AKKAIAMRRV GQSIVETIGG R AIHPVTGV PGGVSKALSE EKRDELLKEI DEMIAYGQDG IALIKSLNEK YMDVVKSLGV IDTWYLGMVK EGKHNFYGDT LR FMSPDGK QTTDFKPSEY LDNIGEHVVG HNYVKYPYNK KVGYPDGLYR VGPLAMLNVC DSMPTPLAEE ARKDFADTFG KPA NQSLAY NHARLIELLA SCERVKELLE DSEITSTDIK AEVEPKAGNG VGAIYAPRGT LFHNYETDDK GIVVKANMIV ASTH NVPTM EKAIQQAAEV VFK

UniProtKB: Coenzyme F420-reducing hydrogenase, alpha subunit

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Macromolecule #5: F420-non-reducing hydrogenase small subunit

MacromoleculeName: F420-non-reducing hydrogenase small subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 30.787498 KDa
SequenceString: MADKVKVGII QLCGCSGCHI SLLDLHEGLL DVLPALEIVY APIIADVKEI PDVDVFLVEG GVRSEHDEHL IHEIREKSKV VIAWGSCAA FGGIPGLGNM YTPEQLKETV YTTVSTDNPG VIPTEGVPEL TTEVRAIPDV VKADYVIPGC PPKPALTAGA I VALLEGKD ...String:
MADKVKVGII QLCGCSGCHI SLLDLHEGLL DVLPALEIVY APIIADVKEI PDVDVFLVEG GVRSEHDEHL IHEIREKSKV VIAWGSCAA FGGIPGLGNM YTPEQLKETV YTTVSTDNPG VIPTEGVPEL TTEVRAIPDV VKADYVIPGC PPKPALTAGA I VALLEGKD PVLPTKIVCD ECPRTKENVF PKEFKRSFEG TPDPEKCLFE QGYTCMGMAT RAGCGAMCPS ANMPCRGCYG KT DETLDQG AAAANTYANA GEAALEIPDK VATLNRFTLP VALVSKKIQK E

UniProtKB: UNIPROTKB: A0A7J9P3N2

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Macromolecule #6: F420-non-reducing hydrogenase subunit delta

MacromoleculeName: F420-non-reducing hydrogenase subunit delta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 14.675697 KDa
SequenceString:
MAEPVIMAFV CYQUGYGAAD LAGTSRMQYP ASVRAIRVPC TGKFDITYAL RAFQKGADAV FVAGUKPNEC AFETGNFKAE ERVKFGKQI LDELGIGGER LEMFFMSGAD AGKFTEAVKE MTDRVKKLGP NPIKA

UniProtKB: F420-non-reducing hydrogenase subunit delta

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Macromolecule #7: F420 non-reducing hydrogenase subunit

MacromoleculeName: F420 non-reducing hydrogenase subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 3.119515 KDa
SequenceString:
MVDEAKLNLI EIVLRAYDPU YSCAAHM

UniProtKB: F420 non-reducing hydrogenase subunit

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Macromolecule #8: formate dehydrogenase (coenzyme F420)

MacromoleculeName: formate dehydrogenase (coenzyme F420) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase (coenzyme F420)
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 74.353594 KDa
SequenceString: MELDFIHTIC PYCGTGCGVD LVVKDGTLVG TNPFKRHPVN EGKTCIKGSY CHEFVHRDDR LKTPLIRKNG ELVEASWDEA LELISGKLQ NYSPEEVGFF SSARCTNEDN YVFQKFARTV IKTNNVDHCA RLUHSATVVG LGQAFGSGAM TNSISDIEDA D CIFIIGSN ...String:
MELDFIHTIC PYCGTGCGVD LVVKDGTLVG TNPFKRHPVN EGKTCIKGSY CHEFVHRDDR LKTPLIRKNG ELVEASWDEA LELISGKLQ NYSPEEVGFF SSARCTNEDN YVFQKFARTV IKTNNVDHCA RLUHSATVVG LGQAFGSGAM TNSISDIEDA D CIFIIGSN TFEQHPLIAR RVVRAKEKGT KIIVIDPRYT PTAKQADLYL QLLPGTNIAV LNAIMHVLVK ENLVDEEFIK NR TKGYEEL KQTLETYTPE YASKLSGVSP ELIVEAAKMY GSANAASILY CMGITQFTTG VNNVKSCCNL AMITGNIGKP GTG VNPLRG QNNVQGACDM GALPNVFPGY QAVPANHEKY AEAWNTCVDP NVGLSIPDML AKAGEQVKCI YVMGENPMVS DPDI HHVEH ALKSLDLLIV QDIFLTETAQ VADVVLPGAS WAEKDGTFSN TERRIQKINK AVDSPGEAIA DWKIVKMLAE KMGQG ELFN FNTAEEVFQE IAKVTPQYAG VTYERLGVDG LHWPCKTCED PGTPILHCEK CLTPDGLGNI FAIDYADPDE MADSEY PMT LTTGRIIFHY HTGTMTRRSK HMADEINEGF VEIHPEDAEK MGIKNKQKVK VSTRRGEVVV NAKITPNIKQ GVVFMPF HF AETAANILTN PAQDPNCKIP EYKVCAAKVE KI

UniProtKB: formate dehydrogenase (coenzyme F420)

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Macromolecule #9: formate dehydrogenase (coenzyme F420)

MacromoleculeName: formate dehydrogenase (coenzyme F420) / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase (coenzyme F420)
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 42.748422 KDa
SequenceString: MSNEMYYVQA SDPAILEKGE CGGAVTALFK YLLDKGIVDG VLALKKGVDV YDAIPTFVTS SEDLLSTAGS LHCAPTMWGG IIKEYLQDA KIAVPVKPCD MRAIVELAKR AQINLDNVYM IGLNCGGTVP PKTAMEMIKL FYEVDPKDVV KEEIDKGKFI I VMKDGSHK ...String:
MSNEMYYVQA SDPAILEKGE CGGAVTALFK YLLDKGIVDG VLALKKGVDV YDAIPTFVTS SEDLLSTAGS LHCAPTMWGG IIKEYLQDA KIAVPVKPCD MRAIVELAKR AQINLDNVYM IGLNCGGTVP PKTAMEMIKL FYEVDPKDVV KEEIDKGKFI I VMKDGSHK EVKMHDLEDN GYGRRVNCQR CDEKIPRKAD IAAGNWGVIG EDAGKYTFME VCTEKGKQLL ESAEKDGYIK KK APNPKGL EIRAKVESSM LKMGEDYKRK WLEEEYPSIE EWNRQWNKCI KCYGCRDVCP VCFCRDCALT ADYVDTGSIP PDP IMFQGV RMSHMAFSCV NCGQCEDVCP MEIPVARIFH KIQEKTRKEL GYRPGVDDEA PPALGGS

UniProtKB: UNIPROTKB: A0A7J9PDY4

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Macromolecule #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 24 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #11: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 11 / Number of copies: 3 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #12: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 12 / 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 #13: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

MacromoleculeName: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / type: ligand / ID: 13 / Number of copies: 1 / Formula: NFU
Molecular weightTheoretical: 194.583 Da
Chemical component information

ChemComp-NFU:
formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

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Macromolecule #14: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 14 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #15: TUNGSTEN ION

MacromoleculeName: TUNGSTEN ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: W
Molecular weightTheoretical: 183.84 Da

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Macromolecule #16: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...

MacromoleculeName: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
type: ligand / ID: 16 / Number of copies: 2 / Formula: MGD
Molecular weightTheoretical: 740.557 Da
Chemical component information

ChemComp-MGD:
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

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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: 7.6
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
12.5 mMMgCl2magnesium chloride
20.0 ?MC27H33N9O15P2flavin adenine dinucleotide
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification under strict anaerobic conditions inside a Coy Lab's vinyl anaerobic chamber (95% N2/ 5% H2).

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 110231
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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