[English] 日本語
Yorodumi
- EMDB-19538: CryoEM structure of the Elp-Hdr complex of Methanothermobacter ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19538
TitleCryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (composite structure)
Map dataCombined focused map of conformational state 1 of the Elp-Hdr flexible arm
Sample
  • Complex: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
    • Protein or peptide: x 6 types
  • Ligand: x 5 types
KeywordsRedox / Flavin-based electron bifurcation / methanogenesis / heterodisulfide reductase / F420-H2 oxidase / Oxidoreductase
Function / homology
Function and homology information


formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate dehydrogenase / methanogenesis / iron-sulfur cluster binding / NADH dehydrogenase activity / respiratory electron transport chain ...formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate dehydrogenase / methanogenesis / iron-sulfur cluster binding / NADH dehydrogenase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal ...F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / 4Fe-4S dicluster domain / Alanine dehydrogenase/PNT, C-terminal domain / 4Fe-4S dicluster domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / 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
Methyl viologen-reducing hydrogenase, subunit D-related protein / formate dehydrogenase (coenzyme F420) / Formate dehydrogenase, alpha subunit / 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
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsSan Segundo-Acosta P / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Altered electron flow in hydrogenotrophic methanogens under nickel limitation
Authors: Nomura S / Shima S / San Segundo-Acosta P / Murphy BJ
History
DepositionFeb 2, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19538.png

Downloads & links

-
Map

FileDownload / File: emd_19538.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined focused map of conformational state 1 of the Elp-Hdr flexible arm
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 448 pix.
= 374.976 Å		0.84 Å/pix.
x 448 pix.
= 374.976 Å		0.84 Å/pix.
x 448 pix.
= 374.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.34
Minimum - Maximum-25.218021 - 41.607883000000001
Average (Standard dev.)0.0016261701 (±1.0470434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 374.976 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : F420-dependent electron-donating proteins- heterodisulfide reduct...

EntireName: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
Components
  • Complex: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: Formate dehydrogenase, beta subunit
    • Protein or peptide: Formate dehydrogenase, alpha subunit
    • Protein or peptide: Methyl viologen-reducing hydrogenase, subunit D-related protein
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: water

+
Supramolecule #1: F420-dependent electron-donating proteins- heterodisulfide reduct...

SupramoleculeName: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 450 KDa

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

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 72.264961 KDa
SequenceString: MAEEKKETME EPKIGVYVCH CGVNIGGVVD VEAVRDYAAK LPNVVIAKDY KYYCSDPGQL EIQKDIKELG INRVVVAACS PRLHEPTFR RCVEEAGLNQ FLFEFANIRE HDSWVHMDNP EGATEKAKDL VRMAVAKARL LEPLEASKVS VDDKALVIGG G VAGIQAAL ...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: Formate dehydrogenase, beta subunit

MacromoleculeName: Formate dehydrogenase, beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 43.387148 KDa
SequenceString: MKYLLARATD EEIQRKGECG GAVTAIFKYM LDKEVVDAVL TLERGYDVYD GIPVLLEDSS GIESTCGSLH CAPTMFGDLI SRYLSDMRL AVAVKPCDAM AIRELEKRHQ IDPDKVYKIG LNCGGTLAPV SAREMIETFY EIDPDDVVSE EIDRGKFIVE L RDGSHREI ...String:
MKYLLARATD EEIQRKGECG GAVTAIFKYM LDKEVVDAVL TLERGYDVYD GIPVLLEDSS GIESTCGSLH CAPTMFGDLI SRYLSDMRL AVAVKPCDAM AIRELEKRHQ IDPDKVYKIG LNCGGTLAPV SAREMIETFY EIDPDDVVSE EIDRGKFIVE L RDGSHREI SIDYLEEEGF GRRENCQRCE IMVPRNADLA CGNWGADDGW TFIEVNTERG QEIIEGARSS GYIEAREPSE KM VKIREKI ENAMISMARK FQDKYLDEEY PSLDEWDEYW KRCINCFACR DACPVCFCRE CELEKDYLLE SDEKAPDPLT FQG VRLSHM GFSCINCGQC EDVCPMDIPI ARIYHRIQKK YRDRTGFTAG VSQELPPMYS GEKD

UniProtKB: formate dehydrogenase (coenzyme F420)

+
Macromolecule #3: Formate dehydrogenase, alpha subunit

MacromoleculeName: Formate dehydrogenase, alpha subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 37.682695 KDa
SequenceString: MMVKHTLCPS CSAGCGVNIV EMGGAPVGTY PYRRHPVNEG KTCRAGRDCY EIPLMDRVTS PGVKKSGKLS GVNWDEALDK LTELLSSED ISILTTGTLT NEEALKLREI IENFNVKKSG LITVFPEFDY PEIDIRNIRD YDNIAVIGDA ITCAPLIGRR I FHAMAAGA ...String:
MMVKHTLCPS CSAGCGVNIV EMGGAPVGTY PYRRHPVNEG KTCRAGRDCY EIPLMDRVTS PGVKKSGKLS GVNWDEALDK LTELLSSED ISILTTGTLT NEEALKLREI IENFNVKKSG LITVFPEFDY PEIDIRNIRD YDNIAVIGDA ITCAPLIGRR I FHAMAAGA EVRSYDRRDE TRMAVNSGFH ITFSDEREVL NDLQQLPGGS LIIITPEIPE IIGPVLEFSS ENEFDVLPIF ED FNTRGVM QHLPPVNEGE FDSVWLIDPG AAAEPVDVSG KFVLQSIRTE GLTPDIFLPV AAWCEKSGSY TSTAGYTMKL EPA LQAPEG VLSDMEIFER ILRAGD

UniProtKB: Formate dehydrogenase, alpha subunit

+
Macromolecule #4: Methyl viologen-reducing hydrogenase, subunit D-related protein

MacromoleculeName: Methyl viologen-reducing hydrogenase, subunit D-related protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 15.550847 KDa
SequenceString:
MSFEPKIVGF CCNWCSYGGA DTAGTARMQY PPNVRIIRVM CSGRVNASMI LKAFSEGADG VFVGGCHIGD CHYDSGNYKW KRRARFIED ILPEFGIDKE RFRWEWISAS EGEKFQKTMQ EFYETVKYLG PLKRAGK

UniProtKB: Methyl viologen-reducing hydrogenase, subunit D-related protein

+
Macromolecule #5: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 33.496371 KDa
SequenceString: MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE ...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 #6: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 20.548727 KDa
SequenceString:
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 #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

+
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

+
Macromolecule #9: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #10: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 10 / Number of copies: 4 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 14 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.6
Details: 50 mM Tris-HCl pH 7.6 containing 400 mM Ammonium sulfate.
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7768 / Average electron dose: 65.0 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: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 76528
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Automated model building using Model Angelo
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8rvy:
CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 1 (composite structure)

+
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