[English] 日本語
Yorodumi
- EMDB-54825: Heterodisulfide reductase-Formylmethanofuran dehydrogenase super-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54825
TitleHeterodisulfide reductase-Formylmethanofuran dehydrogenase super-assembly
Map data
Sample
  • Complex: Eight-megadalton assembly of Heterodisulfide reductase- Vhu Hydrogenase- Formylmethanofuran dehydrogenase
    • Protein or peptide: x 14 types
  • Ligand: x 8 types
KeywordsMethanogenesis / Super-assembly / Flavin-based elctron bifurcation / Heterodisulfide-reductase / Polyferredoxin / Formylmethanofuran dehydrogenase / ELECTRON TRANSPORT
Biological speciesMethanococcus maripaludis S2 (archaea) / Methanococcus maripaludis (archaea) / Methanococcus maripaludis deltae (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
DepositionAug 19, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54825.png

Downloads & links

-
Map

FileDownload / File: emd_54825.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 800 pix.
= 760. Å		0.95 Å/pix.
x 800 pix.
= 760. Å		0.95 Å/pix.
x 800 pix.
= 760. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.084
Minimum - Maximum0.0 - 1.999753
Average (Standard dev.)0.0040742676 (±0.033845086)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

+
Entire : Eight-megadalton assembly of Heterodisulfide reductase- Vhu Hydro...

EntireName: Eight-megadalton assembly of Heterodisulfide reductase- Vhu Hydrogenase- Formylmethanofuran dehydrogenase
Components
  • Complex: Eight-megadalton assembly of Heterodisulfide reductase- Vhu Hydrogenase- Formylmethanofuran dehydrogenase
    • Protein or peptide: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
    • Protein or peptide: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2
    • 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: Ferredoxin
    • Protein or peptide: Formylmethanofuran dehydrogenase subunit A
    • Protein or peptide: Molybdopterin oxidoreductase
    • Protein or peptide: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
    • Protein or peptide: Formylmethanofuran dehydrogenase subunit D
    • Protein or peptide: 4Fe-4S ferredoxin
    • Protein or peptide: 4Fe-4S binding protein
  • 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: TUNGSTEN ION
  • Ligand: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

+
Supramolecule #1: Eight-megadalton assembly of Heterodisulfide reductase- Vhu Hydro...

SupramoleculeName: Eight-megadalton assembly of Heterodisulfide reductase- Vhu Hydrogenase- Formylmethanofuran dehydrogenase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #14, #4-#13
Source (natural)Organism: Methanococcus maripaludis S2 (archaea)
Molecular weightTheoretical: 8 MDa

+
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: 4 / 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

+
Macromolecule #2: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2

MacromoleculeName: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin 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: H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit B2

+
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: 4 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanococcus maripaludis (archaea)
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

+
Macromolecule #4: F420-non-reducing hydrogenase small subunit

MacromoleculeName: F420-non-reducing hydrogenase small subunit / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on hydrogen as donor; With unknown physiological acceptors
Source (natural)Organism: Methanococcus maripaludis deltae (archaea)
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

+
Macromolecule #5: F420-non-reducing hydrogenase subunit delta

MacromoleculeName: F420-non-reducing hydrogenase subunit delta / type: protein_or_peptide / ID: 5 / Number of copies: 4 / 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

+
Macromolecule #6: F420 non-reducing hydrogenase subunit

MacromoleculeName: F420 non-reducing hydrogenase subunit / type: protein_or_peptide / ID: 6 / Number of copies: 4 / 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

+
Macromolecule #7: Ferredoxin

MacromoleculeName: Ferredoxin / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 42.128707 KDa
SequenceString: AGISIQEDAC LVCNACAKAC PTEAIEIAPF KTCIQCFSCA TACPTGALVE KDGKLVFNGS KCDLDGACQK ACPVGIKKVD DRFPYSKGH CVLCEKCVDI CPAEIISLPG KAEKPKKEII IPQEPIAVTK DCVACGVCVP ECPVDAISIE DIAVIDTDKC I YCTVCSQT ...String:
AGISIQEDAC LVCNACAKAC PTEAIEIAPF KTCIQCFSCA TACPTGALVE KDGKLVFNGS KCDLDGACQK ACPVGIKKVD DRFPYSKGH CVLCEKCVDI CPAEIISLPG KAEKPKKEII IPQEPIAVTK DCVACGVCVP ECPVDAISIE DIAVIDTDKC I YCTVCSQT CPWNAIFVAG KLPQKRQKTI KSFTVNEEEC IGCEKCVEAC PGSMIEYNGE KLGVKLPGAC PACGLCVESC PV EVISLEV EYASAKPVTD EGLVWSEEKC AYCGPCAIKC PTGAIKVVNP KGLELPSKKK TEKANEFAMC IRCGACAMKC PTG ALKMGK MVHEGKEYAR VEFSPALCNE CGECVDVCPQ KTLELTGDDK MPLKGYCVMC LKCIEACNKT KKEALSLK

UniProtKB: Ferredoxin

+
Macromolecule #8: Formylmethanofuran dehydrogenase subunit A

MacromoleculeName: Formylmethanofuran dehydrogenase subunit A / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 63.386711 KDa
SequenceString: MEYIIRNGTV FDPLNKVNGE KMDICVKDGK IVESVSKNAL EIDANNKIVM AGGVDSHSHI AGAKVNTGRT LRPEDSKKDL FSKEGLRQG SGFSIPSTFK TGYQYSGMGY TTVIEAAMPP LVARHTHEEF MDLPQIDKAA MPLFGNSWMV LEYLKNGDLS M CAAYVAWL ...String:
MEYIIRNGTV FDPLNKVNGE KMDICVKDGK IVESVSKNAL EIDANNKIVM AGGVDSHSHI AGAKVNTGRT LRPEDSKKDL FSKEGLRQG SGFSIPSTFK TGYQYSGMGY TTVIEAAMPP LVARHTHEEF MDLPQIDKAA MPLFGNSWMV LEYLKNGDLS M CAAYVAWL LRVTKGFAIK IVNPGGTEAW GWGKNVHGLD DEVPYFGITP REIVTGLTKV NEMLGLPHSV HVHPNNLGHP GN WETTIDT MDCVKDIKAK PKFGDRDTVY YNTHLQFHSY GGTSWKDCVS KGVETADYVN KHKHVMIDVG QVTLDETTTM TAD GPMEYD LHMTNGLKWA NCDVELETGS GVVPFIYSPK GPVYSLQWAI GLDIFLYTNP EKLILTTDHP NAGPFIRYPR VIAW LLSKE YRDDWIQNRV HKWAAEKSHI TETDREYSMY DIAQITRANS SKVLGLSGDR GHLGVGAKAD ISIYDIDPEE KSGKK IEKA FLEAAYVLKD GDVVVKNGNV VKEVYGDTIF VNAEINESLE AELLKDLNMK FKKLYSVNME NYPVQDAYAN SWMPIN IDA TEIQ

UniProtKB: UNIPROTKB: A0A7J9NZ09

+
Macromolecule #9: Molybdopterin oxidoreductase

MacromoleculeName: Molybdopterin oxidoreductase / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 48.582508 KDa
SequenceString: IKVEVFKNVV CPFCGTLCDD IEVLVENNHV VGTRNACRIG NAKFMHFEGA VRHESPLMRE NKKDDFKKVD YETATEETAR LLVEAKLPL IYGWSSAECH AQQLGVLLAE KTKAIVDNTA SVUHGPSLLA VQDVGYPVST LGETKNRADV VLFWGSNPMH A HPRHMSRY ...String:
IKVEVFKNVV CPFCGTLCDD IEVLVENNHV VGTRNACRIG NAKFMHFEGA VRHESPLMRE NKKDDFKKVD YETATEETAR LLVEAKLPL IYGWSSAECH AQQLGVLLAE KTKAIVDNTA SVUHGPSLLA VQDVGYPVST LGETKNRADV VLFWGSNPMH A HPRHMSRY SVFPRGFFRQ RGKQDRQMIV VDPRKTDTAK LADIHLQVEP HKDYELVSAL RAAAKGFNIE AEQVAGVPTE TI YEAVDIC KNAQFGSLFF AMGVTMSRGK HRIIDNAIQF VIDMNAYTKF VLTPMRGHYN VNGFNQVSTW VTGYPYGVDF SRG YPRYNP GETASNDVLQ RGDTDMMINV ASDAGAHFPQ KAVQHMAKIP LVCIDPHETP SSVISNIVLP PAITGLEVSG TAYR MDGVP IELRKVIKAP EGMLSDAEIM KMLIKKVDEM K

UniProtKB: UNIPROTKB: A0A2L1CAZ7

+
Macromolecule #10: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C

MacromoleculeName: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 29.204713 KDa
SequenceString: MNELILNLKG DVSVPVEMDK IIPEKIQEMS LEEISGIELI QGNKTAKVSE IFDVELKESP VSKVTINNCC KKVKRIGEKM TSGEIVVNG DAGMYVGVEM KGGKITVNGD AESWVGQNLK GGEIIINGNA ENYVGSAYRG DWRGMSGGKI TITGNAGSEL G EYLKGGTI ...String:
MNELILNLKG DVSVPVEMDK IIPEKIQEMS LEEISGIELI QGNKTAKVSE IFDVELKESP VSKVTINNCC KKVKRIGEKM TSGEIVVNG DAGMYVGVEM KGGKITVNGD AESWVGQNLK GGEIIINGNA ENYVGSAYRG DWRGMSGGKI TITGNAGSEL G EYLKGGTI VIKGNTKIMP GIHQNGGMII IEGDIEGRAG GEMMKGAIVV YGKILEPLPS FKFEGIVEDP LVKLSKKDAG TQ LKGTFIK FSGDYVNTKP KGQLYAAIEN NKNLI

UniProtKB: UNIPROTKB: A0A2L1CC77

+
Macromolecule #11: Formylmethanofuran dehydrogenase subunit D

MacromoleculeName: Formylmethanofuran dehydrogenase subunit D / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: formylmethanofuran dehydrogenase
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 14.159315 KDa
SequenceString:
MKFMLNTGRT IWQGEAIEAG KNLEMYRKAA AVCYMNPEDM DALGVKDGDA IKVISEYGDV AVNAITTDQP APLGMIFIPM GPWANRVVL PDTESTAMPS FKGPLEVEVE KTDEEVLLMS DLMRKAYIE

UniProtKB: UNIPROTKB: A0A2L1CCC1

+
Macromolecule #12: 4Fe-4S ferredoxin

MacromoleculeName: 4Fe-4S ferredoxin / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 38.257918 KDa
SequenceString: MKNFKKDEND GVIEISRSGV EKRVLKWDDC TCVGCGICSE ICPTSAIEMG PLGAIFKGDI DAPKLDISEK CVLCGMCACA CPFDAVKLS INDKPITEMP QYPKIKRGIE LNQSKCVLCE QCELVCPQCA IDVEREVPER KSLVLGEITI KKDDCVLCGI C AEYCPADA ...String:
MKNFKKDEND GVIEISRSGV EKRVLKWDDC TCVGCGICSE ICPTSAIEMG PLGAIFKGDI DAPKLDISEK CVLCGMCACA CPFDAVKLS INDKPITEMP QYPKIKRGIE LNQSKCVLCE QCELVCPQCA IDVEREVPER KSLVLGEITI KKDDCVLCGI C AEYCPADA IELIPNDMNA LSLNPIADIK IDLDACVYCK VCEKACPHNA IEAICYKCPL ASKIKKPELY GEIKGQTNID KD LCVSCGW CANICPADAI EVEKPFEGEL IIDEPACNAC GACISVCPCN ALVFPQPEKQ GDKVPNVVVN QDVCILCGAC THS CPVDAL TVKRTKINMT EANAPAWKKA FSKLMK

UniProtKB: UNIPROTKB: A0A2L1CC83

+
Macromolecule #13: 4Fe-4S binding protein

MacromoleculeName: 4Fe-4S binding protein / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: deltae
Molecular weightTheoretical: 8.35174 KDa
SequenceString:
MYKLEVYPEK CHGCGNCVVA CPVNAQDPDV YGGKGPSSDE KLIMRVENGV VSIVNGDLCG GCGACIEACP VDAIKLVIVK

UniProtKB: UNIPROTKB: A0A2L1CCM5

+
Macromolecule #14: Coenzyme F420-reducing hydrogenase, alpha subunit

MacromoleculeName: Coenzyme F420-reducing hydrogenase, alpha subunit / type: protein_or_peptide / ID: 14 / Number of copies: 4 / 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

+
Macromolecule #15: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 15 / Number of copies: 92 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #16: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 16 / Number of copies: 4 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

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

+
Macromolecule #17: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 17 / Number of copies: 8 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #18: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 18 / Number of copies: 4 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #20: 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: 20 / Number of copies: 4 / 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

+
Macromolecule #21: TUNGSTEN ION

MacromoleculeName: TUNGSTEN ION / type: ligand / ID: 21 / Number of copies: 2 / Formula: W
Molecular weightTheoretical: 183.84 Da

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

MacromoleculeName: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / type: ligand / ID: 22 / Number of copies: 4 / Formula: NFU
Molecular weightTheoretical: 194.583 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
12.5 mMMgCl2magnesium chloride
20.0 uMC27H33N9O15PFlavine-adenine-dinucleotide
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
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).

-
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

+
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more