[English] 日本語
Yorodumi
- EMDB-13258: TmHydABC- T. maritima bifurcating hydrogenase with bridge domain up -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13258
TitleTmHydABC- T. maritima bifurcating hydrogenase with bridge domain up
Map data
Sample
  • Complex: Open bridge conformation TmHydABC bifurcating hydrogenase
    • Protein or peptide: Fe-hydrogenase, subunit alpha
    • Protein or peptide: Fe-hydrogenase, subunit beta
    • Protein or peptide: Fe-hydrogenase, subunit gamma
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: ZINC ION
  • Ligand: water
Function / homology
Function and homology information


hydrogenase (NAD+, ferredoxin) / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding / cytoplasm
Similarity search - Function
NADP-reducing hydrogenase subunit HndA / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. ...NADP-reducing hydrogenase subunit HndA / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Bifurcating [FeFe] hydrogenase beta subunit / Bifurcating [FeFe] hydrogenase alpha subunit / Bifurcating [FeFe] hydrogenase gamma subunit
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria) / Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFurlan C / Chongdar N / Gupta P / Lubitz W / Ogata H / Blaza JN / Birrell JA
Funding support United Kingdom, Germany, Japan, 3 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MR/T040742/1 United Kingdom
German Research Foundation (DFG)BI 2198/1-1 Germany
Japan Society for the Promotion of Science (JSPS)16K21748 Japan
CitationJournal: Elife / Year: 2022
Title: Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase.
Authors: Chris Furlan / Nipa Chongdar / Pooja Gupta / Wolfgang Lubitz / Hideaki Ogata / James N Blaza / James A Birrell /
Abstract: Electron bifurcation is a fundamental energy conservation mechanism in nature in which two electrons from an intermediate-potential electron donor are split so that one is sent along a high-potential ...Electron bifurcation is a fundamental energy conservation mechanism in nature in which two electrons from an intermediate-potential electron donor are split so that one is sent along a high-potential pathway to a high-potential acceptor and the other is sent along a low-potential pathway to a low-potential acceptor. This process allows endergonic reactions to be driven by exergonic ones and is an alternative, less recognized, mechanism of energy coupling to the well-known chemiosmotic principle. The electron-bifurcating [FeFe] hydrogenase from (HydABC) requires both NADH and ferredoxin to reduce protons generating hydrogen. The mechanism of electron bifurcation in HydABC remains enigmatic in spite of intense research efforts over the last few years. Structural information may provide the basis for a better understanding of spectroscopic and functional information. Here, we present a 2.3 Å electron cryo-microscopy structure of HydABC. The structure shows a heterododecamer composed of two independent 'halves' each made of two strongly interacting HydABC heterotrimers connected via a [4Fe-4S] cluster. A central electron transfer pathway connects the active sites for NADH oxidation and for proton reduction. We identified two conformations of a flexible iron-sulfur cluster domain: a 'closed bridge' and an 'open bridge' conformation, where a Zn site may act as a 'hinge' allowing domain movement. Based on these structural revelations, we propose a possible mechanism of electron bifurcation in HydABC where the flavin mononucleotide serves a dual role as both the electron bifurcation center and as the NAD reduction/NADH oxidation site.
History
DepositionJul 23, 2021-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13258.png

Downloads & links

-
Map

FileDownload / File: emd_13258.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.14934593 - 0.2409231
Average (Standard dev.)0.00012105421 (±0.004913924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 270.272 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_13258_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_13258_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13258_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13258_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Open bridge conformation TmHydABC bifurcating hydrogenase

EntireName: Open bridge conformation TmHydABC bifurcating hydrogenase
Components
  • Complex: Open bridge conformation TmHydABC bifurcating hydrogenase
    • Protein or peptide: Fe-hydrogenase, subunit alpha
    • Protein or peptide: Fe-hydrogenase, subunit beta
    • Protein or peptide: Fe-hydrogenase, subunit gamma
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: ZINC ION
  • Ligand: water

-
Supramolecule #1: Open bridge conformation TmHydABC bifurcating hydrogenase

SupramoleculeName: Open bridge conformation TmHydABC bifurcating hydrogenase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 640 KDa

-
Macromolecule #1: Fe-hydrogenase, subunit alpha

MacromoleculeName: Fe-hydrogenase, subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: hydrogenase (NAD+, ferredoxin)
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 72.351391 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKIYVDGREV IINDNERNLL EALKNVGIEI PNLCYLSEAS IYGACRMCLV EINGQITTSC TLKPYEGMKV KTNTPEIYEM RRNILELIL ATHNRDCTTC DRNGSCKLQK YAEDFGIRKI RFEALKKEHV RDESAPVVRD TSKCILCGDC VRVCEEIQGV G VIEFAKRG ...String:
MKIYVDGREV IINDNERNLL EALKNVGIEI PNLCYLSEAS IYGACRMCLV EINGQITTSC TLKPYEGMKV KTNTPEIYEM RRNILELIL ATHNRDCTTC DRNGSCKLQK YAEDFGIRKI RFEALKKEHV RDESAPVVRD TSKCILCGDC VRVCEEIQGV G VIEFAKRG FESVVTTAFD TPLIETECVL CGQCVAYCPT GALSIRNDID KLIEALESDK IVIGMIAPAV RAAIQEEFGI DE DVAMAEK LVSFLKTIGF DKVFDVSFGA DLVAYEEAHE FYERLKKGER LPQFTSCCPA WVKHAEHTYP QYLQNLSSVK SPQ QALGTV IKKIYARKLG VPEEKIFLVS FMPCTAKKFE AEREEHEGIV DIVLTTRELA QLIKMSRIDI NRVEPQPFDR PYGV SSQAG LGFGKAGGVF SCVLSVLNEE IGIEKVDVKS PEDGIRVAEV TLKDGTSFKG AVIYGLGKVK KFLEERKDVE IIEVM ACNY GCVGGGGQPY PNDSRIREHR AKVLRDTMGI KSLLTPVENL FLMKLYEEDL KDEHTRHEIL HTTYRPRRRY PEKDVE ILP VPNGEKRTVK VCLGTSCYTK GSYEILKKLV DYVKENDMEG KIEVLGTFCV ENCGASPNVI VDDKIIGGAT FEKVLEE LS KNG

-
Macromolecule #2: Fe-hydrogenase, subunit beta

MacromoleculeName: Fe-hydrogenase, subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: hydrogenase (NAD+, ferredoxin)
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 68.769406 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MFKNAKEFVQ YANKLKTLRE KKLNGVSIYV CVGTGCTAKG ALKVYSAFEE ELKKRNLLGQ VTLEKIDDDK VTLNRTGCCG RCSSGPLVK IMPYRFFYSN VAPEDVPEIV DRTVLKGEPI ERLFLTDPLT GEKVPRIEDT TLFKNQDFYI MEAIGESECD S IEDYIARS ...String:
MFKNAKEFVQ YANKLKTLRE KKLNGVSIYV CVGTGCTAKG ALKVYSAFEE ELKKRNLLGQ VTLEKIDDDK VTLNRTGCCG RCSSGPLVK IMPYRFFYSN VAPEDVPEIV DRTVLKGEPI ERLFLTDPLT GEKVPRIEDT TLFKNQDFYI MEAIGESECD S IEDYIARS GYESLVKALT SMTPEEIIET VKASGLRGRG GGGFPTGLKW EFTRKAQGDI KFVVCNGDEG DPGAFMNRTL LE RDPHLVL EGMIIAGYAV GAQKGYAYIR AEYPFAVKMF KKAIEDARKL GLLGENILGT GFSFDLEVKE GAGAFVCGEE TAL LASIEG KRGMPRPKPP FPAQSGLWGK PTLINNVETY ANIPRILRDG VENYRKRGTE NSPGTKMFSV AGPLKATGII EVEF GTTLR DIIYNICGGF VEGEEFKAVQ IGGPSGACLS EDFIDMPLDY DTLKKADAMV GSGGIVVITK KTCMVEVARF FLDFT KRES CGKCVPCREG TMQAYNILEK FTHGKATYED LKTLEHLSKT IKTASLCGLG KTAPNPILST LKLFREEYIA HIEGEC PSG MCTAFKKYVI NPDICKGCGL CARSCPQNAI TGERGKPYTI DQEKCVKCGL CASKCPFKAI ELV

-
Macromolecule #3: Fe-hydrogenase, subunit gamma

MacromoleculeName: Fe-hydrogenase, subunit gamma / type: protein_or_peptide / ID: 3
Details: M initiation codon AS is a linker WSHPQFEK strep tag SGGGGG is a linker ENLYFQ is tev sequence SA is a linker
Number of copies: 1 / Enantiomer: LEVO / EC number: hydrogenase (NAD+, ferredoxin)
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 20.941172 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MASWSHPQFE KSGGGGGENL YFQGAVLALE RHFEKVEEIL KKYGYKRENL IKILLEIQEI YRYLPEDVIN YVSTAMGIPP AKIYGVATF YAQFSLKPKG KYTIMVCDGT ACHMAGSPEV LKAIEEETGL TPGNVTEDLM FSLDQVGCLG ACALAPVMVI N GEVYGNLT ADKVKEILRK IKEKERESAN V

-
Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 7 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

-
Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 5 / Number of copies: 3 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

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

-
Macromolecule #6: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 157 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationName
10.0 mMTris hydrochloride
150.0 mMNaClSodium chloride
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified by gel filtration

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 60700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 4790 / Average exposure time: 6.0 sec. / Average electron dose: 57.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 885306
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hea

Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1) / Details: SGD
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 245000
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7p92:
TmHydABC- T. maritima bifurcating hydrogenase with bridge domain up

+
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