EMDB-55299: Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marbu...

Basic information

Entry

Database: EMDB / ID: EMD-55299

• Title: Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure)
• Map data: Composite map of the Mvh-Hdr-Fmd complex

Sample

• Complex: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis
  • Protein or peptide: x 12 types
• Ligand: x 11 types

• Keywords: Oxidoreductase / hydrogenase / dehydrogenase / polyferredoxin

Function / homology

Function:

formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors / H2:CoB-CoM heterodisulfide,ferredoxin reductase / methanogenesis, from carbon dioxide / CoB--CoM heterodisulfide reductase activity / methanogenesis / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdenum ion binding / ferredoxin hydrogenase activity / molybdopterin cofactor binding / nickel cation binding / iron-sulfur cluster binding / NADH dehydrogenase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane

Domain/homology:

Formylmethanofuran dehydrogenase, fused subunit C/D / 4Fe-4S binding domain / FwdD/FmdC, molybdopterin dinucleotide-binding domain / : / : / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / : / 3Fe-4S ferredoxin / Glutamate synthase, alpha subunit, C-terminal domain superfamily / : / MnmG, N-terminal domain / Glucose inhibited division protein A / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / F420-non-reducing hydrogenase iron-sulfur subunit D / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / Cysteine-rich domain / Amidohydrolase 3 / Amidohydrolase family / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / : / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenase, large subunit, nickel binding site / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Alpha-helical ferredoxin / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Metal-dependent hydrolase, composite domain superfamily / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Aspartate decarboxylase-like domain superfamily / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / Metal-dependent hydrolase / 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

Component:

Tungsten formylmethanofuran dehydrogenase, subunit F / Tungsten formylmethanofuran dehydrogenase, subunit G / Tungsten formylmethanofuran dehydrogenase, subunit A / formylmethanofuran dehydrogenase subunit B / F420-non-reducing hydrogenase subunit A / Polyferredoxin protein MvhB / F420-non-reducing hydrogenase iron-sulfur subunit D / F420-non-reducing hydrogenase subunit G / Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

• Biological species: Methanothermobacter marburgensis (archaea)
• Method: single particle reconstruction / cryo EM / Resolution: 2.7 Å
• Authors: San Segundo-Acosta P / Murphy BJ

Funding support

Germany, 1 items

Organization	Grant number	Country
Max Planck Society		Germany

• Citation: Journal: Science Advances / Year: 2026; Title: Diversity of electron-bifurcating CO2-fixing supercomplexes in methanogens; Authors: San Segundo-Acosta P / Nomura S / Fernandes-Queiroz JP / Protasov E / Kahnt J / Kaneko M / Hochberg G / Shima S / Murphy BJ

History

Deposition	Oct 4, 2025	-
Header (metadata) release	Apr 29, 2026	-
Map release	Apr 29, 2026	-
Update	Apr 29, 2026	-
Current status	Apr 29, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_55299.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Composite map of the Mvh-Hdr-Fmd complex
• Voxel size: X=Y=Z: 0.83563 Å

Density

Contour Level	By AUTHOR: 4.2
Minimum - Maximum	-28.133669999999999 - 50.92418
Average (Standard dev.)	0.012208479 (±0.9164779)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 480 480 480 Spacing 480 480 480
Cell	A=B=C: 401.1 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzym...

• Entire: Name: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis

Components

• Complex: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis
  • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
  • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
  • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
  • Protein or peptide: F420-non-reducing hydrogenase iron-sulfur subunit D
  • Protein or peptide: F420-non-reducing hydrogenase subunit G
  • Protein or peptide: Tungsten formylmethanofuran dehydrogenase, subunit F
  • Protein or peptide: Tungsten formylmethanofuran dehydrogenase, subunit A
  • Protein or peptide: formylmethanofuran dehydrogenase subunit B
  • Protein or peptide: Tungsten formylmethanofuran dehydrogenase, subunit G
  • Protein or peptide: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C
  • Protein or peptide: Polyferredoxin protein MvhB
  • Protein or peptide: F420-non-reducing hydrogenase subunit A
• Ligand: IRON/SULFUR CLUSTER
• Ligand: FLAVIN-ADENINE DINUCLEOTIDE
• Ligand: Non-cubane [4Fe-4S]-cluster
• Ligand: FE2/S2 (INORGANIC) CLUSTER
• Ligand: ZINC 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
• Ligand: MOLYBDENUM ATOM
• Ligand: HYDROSULFURIC ACID
• Ligand: FE3-S4 CLUSTER
• Ligand: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
• Ligand: water

Supramolecule #1: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzym...

• Supramolecule: Name: (MvhABGD-HdrABC)2-(FmdABCDG)4 flavin-bifurcating CO2-fixing enzyme megacomplex of Methanothermobacter marburgensis; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 1.2 MDa

Macromolecule #1: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

• Macromolecule: Name: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A; type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 72.264961 KDa

Sequence

String:

MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP EGATEKAKDL VRMAVAKARL LEPLEASKVS VDDKALVIGG G VAGIQAAL DLADMGFKTY MVEKRPSISG RMGQLDKTFP TLDCSMCILA PKMVDVGKHD NIELITYAEV KEVDGYIGNF KV KIEKKPR YIDEELCTGC GSCVEVCPIE MPNYFDEGIG MTKAVYIPFP QAVPLCATID KDYCIECMLC DEVCERGAVK HDQ EPEEIE IEVGTIIVAT GYDAYDPTEK LEYGYGRHTN VITGLELERM INASGPTDGK VLKPSDGEKP KRVAFIHCVG SRDE QIGKP YCSRVCCMYI MKNAQLIKDK MPDTEVTLYY MDIRAFGKGF EEFYKRSQEK YGIKFIRGRP AEVIENPDLT LTVRS EDTL LGKVTEYDYD MVVLGVGLVP PEGAETLRQT IGLSKSADGF LMEAHPKLRP VDTLTDGVYL AGVAQGPKDI PDAVAQ ASG AAARAAIPMV KGEVEIEPII AVTDSDVCGG CEVCIELCPF GAISIEEGHA NVNVALCKGC GTCVAACPSG AMDQQHF KT EQIMAQIEAA LNEPASK

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

Macromolecule #2: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

• Macromolecule: Name: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B; type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 33.496371 KDa

Sequence

String:

MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE RPTILDEIVE VTGAKSVEYK DKMMCCGAGG GVRSRDLDVA LDFTREKLTN MKEAGVDAIV NVCPFCHLQF DV GQMEIKD KFGEEFDIPV LHLAQLLGLA MGLPKEDLVV DAHQVCVDEC LEKLEELDRL APGSG

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

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

• Macromolecule: Name: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C; type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 20.548727 KDa

Sequence

String:

MTLLQREENI IRKGNIDKEF SEKIKAAGGD SLEYCFQCGT CTGSCPSGRR TPYRVRQIIR KANVGLKDEI ISDPTLWMCT TCYSCQERC PRKVKIVDVV KLARNEAAKA GFMAPAHKAV GSFVIKTGHG VPINDATMEL RKAVGLGELP PTTHQFPEAL E EVQKIIKA TGFDQLIGYN WETGELE

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

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

• Macromolecule: Name: F420-non-reducing hydrogenase iron-sulfur subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO; EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 15.954442 KDa

Sequence

String:

MAEDDIKIVM FCCNWCSYGG ADTAGTARMQ YPTNIRVIRV MCSGRIEPQF VFKAFREGAD GVLVTGCHHG DCHYDAGNYK LDRRMRLIY KLADELGIGR ERIHHDWISA SEGEKFAETV KMMVDRIRAL GPSPIKKQLA EA

UniProtKB: F420-non-reducing hydrogenase iron-sulfur subunit D

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

• Macromolecule: Name: F420-non-reducing hydrogenase subunit G / 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: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 33.786582 KDa

Sequence

String:

MAEKIKIGTM WLGGCSGCHL SIADFHEKLL DVMEHADFEF SPVLMDTKYD EIPELDVVVI EGGIVNDENR EFAEELREKA KFVISYGTC AVYGGIPGLR NLWDKDEVIE EAYINSITTP NEEGVIPSED VPHLEGRVKP LGEVIDVDFE VPGCPPRSDV A AEVVMALL KGEEIELPST NLCEVCPREK PPEGLAMDFI KRQFEVGKPE DDLCLIPQGL ICMGPATVSI CGAECPSIAI PC RGCYGPT ARVEDQGAKM ISAIASDYKV EEDKTVDPEE VAEQLDDIVG TFYTFTLPAA LIPMKIKKEG K

UniProtKB: F420-non-reducing hydrogenase subunit G

Macromolecule #6: Tungsten formylmethanofuran dehydrogenase, subunit F

• Macromolecule: Name: Tungsten formylmethanofuran dehydrogenase, subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 38.614516 KDa

Sequence

String:

METTEVIEGK NITVERTGEE NRKLIFQDCL CAVCGLCGEI CPVSAIEVNP TGAMVRTEQD ESKILIDENK CVLCGMCSSI CPFQALDLQ IDGTSIKELA EYPKILKSAE IDDETCIQCK ACETACPQDA ITITRELPER KDLITGEIEI DKDTCIYCGM C EEMCPVDA IEIEHQIPSS SSPTVATDIN VDEDKCVHCG ICKRICPVDA IMQVCRICPY GEYEIKVPEV TGTSYIDPEL CV NCGWCQE ICPVDAATVT KPFEGELIID QDTCQACETC VMACPCNVLS FPKPEKSGEK PTKLYKDERF CIYCGACERS CPV NAIEVK RSRINTTPIK SKAWKNAFES LLK

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit F

Macromolecule #7: Tungsten formylmethanofuran dehydrogenase, subunit A

• Macromolecule: Name: Tungsten formylmethanofuran dehydrogenase, subunit A / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 63.00182 KDa

Sequence

String:

MEYIIKNGFV YCPLNNVDGE KMDICVRDGK IVESVSDSAK VIDASGKIVM PGGVDPHSHI AGAKVNVGRM YRPEDSRRDA EKFKAGRAG SGFSVPSTFM TGYRYAQMGY TTAMEAAMPP LLARHTHEEF HDTPIIDHAA YPLFGNNWFV MEYLKEGDVD A CAAYASWL LKATKGYTI(KCX) IVNPAGTEAW GWGGNVHGIH DPAPYFDITP AEIIKGLAEV NEKLQLPHSI HLHCNDLG H PGNYETTLAS FDVPKNIKAN PATGERDTVL YATHVQFHSY GGTTWRDFVS EAPKIADYVN KNDHIVIDVG QITLDETTT MTADGPMEYD LHSLNGLKWA NCDVELETGS GVVPFIYSAR APVPAVQWAI GMELFLLIDD PAKVCLTTDS PNAGPFTRYP RVIAWLMSN KYRMNLIEGE LHKWAQRKST IATVDREYTF SEIAQITRST SAKVLGLSET KGHLGVGADA DIAVYNINPE T VDPSVDYM AIEEGFSRAA YVLKDGEIVV KDGEVVASPH GRTYWVDTRV DESTYNEVLA KVESKFKQYY SVNFANYPVQ DE YLPKSAP VKGVML

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit A

Macromolecule #8: formylmethanofuran dehydrogenase subunit B

• Macromolecule: Name: formylmethanofuran dehydrogenase subunit B / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 48.179773 KDa

Sequence

String:

MSVYKNVTCP VCGGSCDDIE VLYDGKTIKT RNACRMGNAK FQEMVSSHRI LRPQIKTESG FRSAEWDEAL DAAAEILTES KRPTLFMGS EMSTEAMAAG LELGEYLNAM VDSNATICHG PTLMGIQEAG QSAATAGEIK NRADVIIYWG TNVMDSMPRH M SRYSIFMR GFFRERGKKD RTVISVDPRE TATTKASDIH LQLKPNSDYE LFSALLTVIR GNEPHRSIES ITGISVETIK EV ADIMLNA QFGAIYGGLG LASSEGKHRN VEMVLKLVAA LNEHTKFTIG AIRGHCNVAG FNQVASWEYG FPFGVDFTRG YPR YNPGET TIVDLLQRKE SDAVLVICSD LGAHLPKECV EYMKEIPVIC IDIAPCPTTL VSDVVIPGVI DAMESSGTFY RFDN VPIHH KAFTTSPFPE TESNEHTLRQ ILERVKSIKG E

UniProtKB: formylmethanofuran dehydrogenase subunit B

Macromolecule #9: Tungsten formylmethanofuran dehydrogenase, subunit G

• Macromolecule: Name: Tungsten formylmethanofuran dehydrogenase, subunit G / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 8.564948 KDa

Sequence

String:

MAIGLKAYPE LCHGCGNCVI ACPVNALRSP EVAGGKGPTD DVEIIMIVED GVVNIKNPDL CGKCGTCVES CPVDAIRLEE LE

UniProtKB: Tungsten formylmethanofuran dehydrogenase, subunit G

Macromolecule #10: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C

• Macromolecule: Name: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C; type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 43.383215 KDa

Sequence

String:

MGFVLVPKSD FQIPLEADTI RPDLFEGLDL DEIRSLQVYE GNIKRPLGEF FEIAETSHED QLIRIDGDVS RVKYIGSGMK SGKIIINGD VGLQLGCEMK GGEIEVNGNV SSWIGMEMHG GTIKINGNAG DYVGCAYRGE WRGMKGGKII IQGNAGNNIG G GMMAGEIY IGGDAGNFCG IRMNGGEITV RGDAGRAPGA EMVSGIIKIH GRISSLLPGF KEISTFKEDG SLMILFKGDL SE KNPEGNL YINYNKNLHI LENETDEGRV ITKKGIKVIY NSGSTIREGQ IIKGGNKLTD DYIDECARCC ISPEDYKLLG EPE NVVVSS HGNEVVLRAV EDPGIQMGTI FIPRGIWANV LTPPYTESTG SPMYKGVPVY LRKASQGERI LSAEELVEEY GVGK

UniProtKB: Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C

Macromolecule #11: Polyferredoxin protein MvhB

• Macromolecule: Name: Polyferredoxin protein MvhB / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 44.09043 KDa

Sequence

String:

MIVVNKEDCI RCGACQGTCP TAAIEVTPED VIYCDICGGE PKCVDACPTG ALKIEDLVVD EAGNTQGRIV FNPDKCNECG DCVEVCPPQ ILKLDEGKVK KIPLQGFCVM CQKCVDICPV GVIGVEGIKE PAKVELEIEG PIFIADCVGC GMCVPECPVD A ITLEKVGG VIEIDEDTCI KCGVCAQTCP WNAVYISGKK PEKRAKEIRK FELDEEACIG CNTCVEACPG DFIVPKSSNL TV ELPAICT ACGLCEQLCP VDAIDLDVEL GPAKPASEEG LVWDEGKCDF IGACANICPN DAIRVVTREG MKLPDNEKVD EEP SFAMCT RCGACTMACP KGALSLVDMD KVIDGEVVKR KRVQYNPALC DQCGDCIEAC PYDMLKLTDE KVPLKGFCIL CDQC IPACP KGALSLK

UniProtKB: Polyferredoxin protein MvhB

Macromolecule #12: F420-non-reducing hydrogenase subunit A

• Macromolecule: Name: F420-non-reducing hydrogenase subunit A / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO; EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
• Source (natural): Organism: Methanothermobacter marburgensis (archaea)
• Molecular weight: Theoretical: 52.905051 KDa

Sequence

String:

MVKLTMEPVT RIEGHAKITV HLDDAGNVED TRLHVMEFRG FEKFLQGRPI EEAPRIVPRI CGICDVQHHL AAAKAVDACF GFEPDDVLP AAYKMREIMN WGSYMHSHGL HFYFLAAPDF IAGKDRKTRN VFQIIKDAPD VALQAIELRK NALEIVRATG G RPIHPTSS TPGGISTELD DETQKDLLQK AQRNVELAEA TLELAVPIFE ENIDLVNSLG NIETYHTGLV KNGVWDVYDG IV RIKDKEG NLFREFKPAD YADTIAEHVK PYSWLKFPYI KDLGYPDGVY RVSPLSRLNV ADKMPDAAPK AQDYFKEFQD KFG YAQQTL LYHWARLIEV LACAECAADA LEGDLSGEKF PDSLERQAGD GVGIVEAPRG TLTHHYTCDE NGLITKANIV VATI QNNPA MEMGIQKVAQ DYIKPGVEVD DKIFNLMEMV IRAYDPCLSC ATHTIDSQMR LATLEVYDSE GDLVKRI

UniProtKB: F420-non-reducing hydrogenase subunit A

Macromolecule #13: IRON/SULFUR CLUSTER

• Macromolecule: Name: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 45 / Formula: SF4
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

Macromolecule #14: FLAVIN-ADENINE DINUCLEOTIDE

• Macromolecule: Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 14 / Number of copies: 1 / Formula: FAD
• Molecular weight: Theoretical: 785.55 Da

Chemical component information

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

Macromolecule #15: Non-cubane [4Fe-4S]-cluster

• Macromolecule: Name: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 15 / Number of copies: 2 / Formula: 9S8
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

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

Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER

• Macromolecule: Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 16 / Number of copies: 1 / Formula: FES
• Molecular weight: Theoretical: 175.82 Da

Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

Macromolecule #17: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 17 / Number of copies: 4 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #18: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...

• Macromolecule: Name: 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: 18 / Number of copies: 4 / Formula: MGD
• Molecular weight: Theoretical: 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

Macromolecule #19: MOLYBDENUM ATOM

• Macromolecule: Name: MOLYBDENUM ATOM / type: ligand / ID: 19 / Number of copies: 2 / Formula: MO
• Molecular weight: Theoretical: 95.94 Da

Chemical component information

ChemComp-MO:
MOLYBDENUM ATOM

Macromolecule #20: HYDROSULFURIC ACID

• Macromolecule: Name: HYDROSULFURIC ACID / type: ligand / ID: 20 / Number of copies: 2 / Formula: H2S
• Molecular weight: Theoretical: 34.081 Da

Chemical component information

ChemComp-H2S:
HYDROSULFURIC ACID

Macromolecule #21: FE3-S4 CLUSTER

• Macromolecule: Name: FE3-S4 CLUSTER / type: ligand / ID: 21 / Number of copies: 1 / Formula: F3S
• Molecular weight: Theoretical: 295.795 Da

Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

Macromolecule #22: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

• Macromolecule: Name: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / type: ligand / ID: 22 / Number of copies: 1 / Formula: NFU
• Molecular weight: Theoretical: 195.591 Da

Chemical component information

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

Macromolecule #23: water

• Macromolecule: Name: water / type: ligand / ID: 23 / Number of copies: 343 / Formula: HOH
• Molecular weight: Theoretical: 18.015 Da

Chemical component information

ChemComp-HOH:
WATER

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 1.2 mg/mL
• Buffer: pH: 7.6
• Vitrification: Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
• Details: The buffer is pH 7.6 100 mM sodium phosphate with 150 mM NaCl, and containing 2 mM DTT

Electron microscopy

• Microscope: TFS KRIOS
• Specialist optics: Energy filter - Name: TFS Selectris X
• Image recording: Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 18777 / Average exposure time: 3.55 sec. / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 917008
• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: NONE
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC; Details: Particles had been C2-symmetry expanded. It is a composite map; Number images used: 722594
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final 3D classification: Number classes: 2 ; Details: 3D-classification without alignment with RELION used before final local refinements and CTF correction

Atomic model buiding 1

• Initial model: Chain - Source name: Other / Chain - Initial model type: other / Details: Generated using ModelAngelo
• Refinement: Space: REAL / Protocol: RIGID BODY FIT

Output model

PDB-9sw6:
Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure)