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- EMDB-25633: Structure of electron bifurcating Ni-Fe hydrogenase complex HydAB... -

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Entry
Database: EMDB / ID: EMD-25633
TitleStructure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state
Map dataElectron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state
Sample
  • Complex: NiFe hydrogenase complex ABCSL
    • Protein or peptide: NiFe hydrogenase subunit A
    • Protein or peptide: NiFe hydrogenase subunit B
    • Protein or peptide: NiFe hydrogenase subunit C
    • Protein or peptide: NiFe hydrogenase large subunit
    • Protein or peptide: NiFe hydrogenase small subunit
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: NICKEL (III) ION
  • Ligand: CARBONMONOXIDE-(DICYANO) IRON
Keywordshydrogenase complex / electron bifurcation / OXIDOREDUCTASE
Function / homology
Function and homology information


ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / 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
Similarity search - Function
: / NADP-reducing hydrogenase subunit HndA / Soluble ligand binding domain / SLBB domain / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit ...: / NADP-reducing hydrogenase subunit HndA / Soluble ligand binding domain / SLBB domain / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like 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 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 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
Coenzyme F420-reducing hydrogenase, alpha subunit / Coenzyme F420-reducing hydrogenase, gamma subunit / Putative anaerobic dehydrogenase / NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit / NADH-quinone oxidoreductase, E subunit
Similarity search - Component
Biological speciesAcetomicrobium mobile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFeng X / Li H
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase.
Authors: Xiang Feng / Gerrit J Schut / Dominik K Haja / Michael W W Adams / Huilin Li /
Abstract: Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents ...Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents the fourth group, but its bifurcation site is unknown. We report cryo-EM structures of the related NiFe-HydABCSL hydrogenase that reversibly oxidizes H and couples endergonic reduction of ferredoxin with exergonic reduction of NAD. FMN surrounded by a unique arrangement of iron sulfur clusters forms the bifurcating center. NAD binds to FMN in HydB, and electrons from H via HydA to a HydB [4Fe-4S] cluster enable the FMN to reduce NAD. Low-potential electron transfer from FMN to the HydC [2Fe-2S] cluster and subsequent reduction of a uniquely penta-coordinated HydB [2Fe-2S] cluster require conformational changes, leading to ferredoxin binding and reduction by a [4Fe-4S] cluster in HydB. This work clarifies the electron transfer pathways for a large group of hydrogenases underlying many essential functions in anaerobic microorganisms.
History
DepositionDec 6, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7t2r
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25633.png

Downloads & links

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Map

FileDownload / File: emd_25633.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 260 pix.
= 267.54 Å		1.03 Å/pix.
x 260 pix.
= 267.54 Å		1.03 Å/pix.
x 260 pix.
= 267.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.029 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0017738116 - 2.5135465
Average (Standard dev.)0.0030726038 (±0.03870402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 267.54 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z267.540267.540267.540
α/β/γ90.00090.00090.000
start NX/NY/NZ138136120
NX/NY/NZ121111179
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0022.5140.003

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Supplemental data

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Sample components

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Entire : NiFe hydrogenase complex ABCSL

EntireName: NiFe hydrogenase complex ABCSL
Components
  • Complex: NiFe hydrogenase complex ABCSL
    • Protein or peptide: NiFe hydrogenase subunit A
    • Protein or peptide: NiFe hydrogenase subunit B
    • Protein or peptide: NiFe hydrogenase subunit C
    • Protein or peptide: NiFe hydrogenase large subunit
    • Protein or peptide: NiFe hydrogenase small subunit
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: NICKEL (III) ION
  • Ligand: CARBONMONOXIDE-(DICYANO) IRON

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Supramolecule #1: NiFe hydrogenase complex ABCSL

SupramoleculeName: NiFe hydrogenase complex ABCSL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: NiFe hydrogenase subunit A

MacromoleculeName: NiFe hydrogenase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 76.799648 KDa
SequenceString: MKEITLTIDG KVCKGVQGDT ILDVANKNDV YIPTLCYQKG LTPIGACRMC VVQLEGNPKM LPSCTTPAQD GMVVVTKNEK LKDYRRQIL ELLFAGRNHF CMYCSQSGDC ELQRLAIEHE MDSVRFPYLY EDFEVDATDP NLMMDHNRCV LCQRCIRTCS E IVGAHTLD ...String:
MKEITLTIDG KVCKGVQGDT ILDVANKNDV YIPTLCYQKG LTPIGACRMC VVQLEGNPKM LPSCTTPAQD GMVVVTKNEK LKDYRRQIL ELLFAGRNHF CMYCSQSGDC ELQRLAIEHE MDSVRFPYLY EDFEVDATDP NLMMDHNRCV LCQRCIRTCS E IVGAHTLD LERRGWQAKV IADLGKRLRE SDTCVNCGAC AQSCPTGTIT IREFAYRGRR SECDAVVESV CPLCAVGCKI KT YVRTGSI VRVEGTGVEE PDGGQLCHMG RWWLPESTER ERVTVPLIRE GASYREATWE EALALASAEF KKAYDQEKAG AIL SSLCTD EELTLFSALF RNALKMKHID TFDGDIIRGF FKGFMPFREQ GVRPFTAAHH ILDSDLIITM FADPQKEAPV VASY IRVAC LHRNAKLMNL SYGPSPFPGL VDLDIRLPEG QAVPKALSNL AEIIGKISLG PSDMASFGEF EAGAGKALSS YRESI EESA RAMGLDPKIA EEVALMLISA RRPIFIIGGR ATKSHELVTA ACNLAVASKA FFEDGLGVVP LLVSANSLGA RNTVVS ENP WLGRERRDFL YVFSTAMVPE EEEILAAISA TRFVVVQTPF KVRPLVNLAD ILLPAPAWYE RSGHFCTIEG ERRKLNT IV PPKGEIKSLH YVMDEFAKKL GVKLERPEVS PCEEIFKSQL RASEARIVTL

UniProtKB: Putative anaerobic dehydrogenase

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Macromolecule #2: NiFe hydrogenase subunit B

MacromoleculeName: NiFe hydrogenase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 65.557148 KDa
SequenceString: MAIYRAHVLV CRGTGCTASG APGVMKAFKE ELAKKGLDRE VMLVETGCHG MCEMGPVVVV YPEGAFYCRV TPEDVPEIVE EHLYKGRIV QRLLYTVPED MEKVPYYKDI PFYSKQHRIV LSNCGYIDPE KIEEYIARDG YMALGKALLE MTPEEVLEEV K KSGLRGRG ...String:
MAIYRAHVLV CRGTGCTASG APGVMKAFKE ELAKKGLDRE VMLVETGCHG MCEMGPVVVV YPEGAFYCRV TPEDVPEIVE EHLYKGRIV QRLLYTVPED MEKVPYYKDI PFYSKQHRIV LSNCGYIDPE KIEEYIARDG YMALGKALLE MTPEEVLEEV K KSGLRGRG GAGFPTGLKW EFAKKASGDK KYVICNADEG DPGAFMDRST LEGDPHSVIE GMTIGAYVIG ADEGYIYCRA EY PLAIKRL KIAIAQAEEM GLLGDHIMGT NFSFHLHLKE GAGAFVCGEE TALMASIEGR RGMPRPRPPF PAQHGLWGKP TNI NNVETW ANVPRIILNG ADWFASMGTE KSKGTKIFAL TGKITNTGLI EVPMGITIRE IIYELGGGIL NGKEFKAVQI GGPS GGCLT KEHLDLPIDY ESLTAAGAIM GSGGLVVMDE DTCMVDVAKF FLEFTQRESC GKCVPCREGT KQMLLMLQKI CNGEG TMDD LSKLEELAHM VKETSLCGLG QTAPNPVITT IRYFRDEYVA HIKDKRCPAK ICPALIKYVV DPEKCRKCGL CARNCP VKC ISGDRQTPYL INQEKCIKCG TCMQVCPFGA IGKV

UniProtKB: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit

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Macromolecule #3: NiFe hydrogenase subunit C

MacromoleculeName: NiFe hydrogenase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 17.482477 KDa
SequenceString:
MALSTVDVVE KVKEIVAPWK GKQGGLIPIL QEVQRELGYL PEEALLTISR ELKMPKAEVY GVATFYAQFH LKPRGRHVIR VCRGTACHV RGSLQILEKV KQMLGIEENE TTDDLRFTLE PVACLGACGL APVMMVDEDT HGRMTPDKIQ AILDKYQ

UniProtKB: NADH-quinone oxidoreductase, E subunit

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Macromolecule #4: NiFe hydrogenase large subunit

MacromoleculeName: NiFe hydrogenase large subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 53.294242 KDa
SequenceString: MTEVFKLEIN PVTRIEGHGK ITVMLDESGH VRETRFHVTQ YRGFEVFTHG RDFREMPVIT PRICGICPVS HHLASAKACD EILGVTITP AAHKLRELMH MGQIVQSHAL SFFHLSSPDI LWGFDAPVKI RNVAGLVDRY PELAKKGIML RKFGQEIIKT L GGKKIHPW ...String:
MTEVFKLEIN PVTRIEGHGK ITVMLDESGH VRETRFHVTQ YRGFEVFTHG RDFREMPVIT PRICGICPVS HHLASAKACD EILGVTITP AAHKLRELMH MGQIVQSHAL SFFHLSSPDI LWGFDAPVKI RNVAGLVDRY PELAKKGIML RKFGQEIIKT L GGKKIHPW HSIPGGVNRS LTPQERDAIA AQLPEMKSIA MEAIKLIKDY LQEGGEELKE FATLDTAYMG LVRDGYLELY DG EVRIKAP RGRILDQFDP KDYLDHIGEH VEPWSYLKFP FYKALGFPHG SYRVGPLARL NAADAVSTPE ASKEFALYKE MGE DGIVPY TLYYHYARLI EALYGLERIE QLLADPDITS SDLRVTSKEI NPEGIGVIEA PRGTLIHHYQ VNESGVITKV NLIV ATGHN NFAMNKGVEM VAKKYITGTN VPEGVFNRLE HVIRAYDPCL SCSTHAVGKM PLKLELVGPT GEILKEVTRD

UniProtKB: Coenzyme F420-reducing hydrogenase, alpha subunit

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Macromolecule #5: NiFe hydrogenase small subunit

MacromoleculeName: NiFe hydrogenase small subunit / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 19.96516 KDa
SequenceString:
MAKAKVATFW LEACAGCHMS FLDLDERLID LFQNVEILFS PIVDAKDIPN IDVGVLSGGL GNVEEVELAK KMRERCKYLV AWGDCAVFG GINCMRNFIP KDVVLREGYI ETASTVNPQG IVPSEDIPEL LPRALPIDYE VKVDVYVPGC PPDADTIYYV F KELLAGRV PKVPSEMMRY D

UniProtKB: Coenzyme F420-reducing hydrogenase, gamma subunit

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Macromolecule #6: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 12 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #8: NICKEL (III) ION

MacromoleculeName: NICKEL (III) ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: 3NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-3NI:
NICKEL (III) ION

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Macromolecule #9: CARBONMONOXIDE-(DICYANO) IRON

MacromoleculeName: CARBONMONOXIDE-(DICYANO) IRON / type: ligand / ID: 9 / Number of copies: 2 / Formula: FCO
Molecular weightTheoretical: 135.89 Da
Chemical component information

ChemComp-FCO:
CARBONMONOXIDE-(DICYANO) IRON

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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: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
300.0 mMNaclSodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 76.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 269151
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7t2r:
Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state

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