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- EMDB-76459: Cryo-EM density of the [NiFe]-hydrogenase HoxEFU diaphorase subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-76459
TitleCryo-EM density of the [NiFe]-hydrogenase HoxEFU diaphorase subcomplex
Map data
Sample
  • Complex: [NiFe]-hydrogenase HoxEFU diaphorase subcomplex
    • Complex: [NiFe]-hydrogenase HoxE subunit
      • Protein or peptide: [NiFe]-hydrogenase HoxE subunit
    • Complex: [NiFe]-hydrogenase HoxF subunit
      • Protein or peptide: [NiFe]-hydrogenase HoxF subunit
    • Complex: [NiFe]-hydrogenase HoxU subunit
      • Protein or peptide: [NiFe]-hydrogenase HoxU subunit
Keywordsdiaphorase module / electron transfer complex / iron-sulfur cluster protein / [NiFe]-hydrogenase subcomplex / OXIDOREDUCTASE
Function / homology
Function and homology information


NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
NAD-reducing hydrogenase, HoxS gamma subunit / NADP-reducing hydrogenase subunit HndA / Soluble ligand binding domain / SLBB domain / : / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain ...NAD-reducing hydrogenase, HoxS gamma subunit / NADP-reducing hydrogenase subunit HndA / Soluble ligand binding domain / SLBB domain / : / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / 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:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / 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 / Nuo51 FMN-binding 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
Hydrogenase subunit / Hydrogenase subunit / Potential NAD-reducing hydrogenase subunit
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsZiegler SJ / Gruber JN
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Cell Rep Phys Sci / Year: 2026
Title: Cryo-EM map and functional electron transport studies of the HoxEFU sub-complex of the HOX [NiFe]-hydrogenase from Synechocystis sp. PCC 6803
Authors: Dawson ME / Kisgeropoulos EC / Gruber JN / Ziegler SJ / Bharadwaj VS / Dahl PJ / Blahut MR / Wiley SA / Artz JH / Lubner CE / Mulder DW / King PW
History
DepositionApr 7, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76459.png

Downloads & links

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Map

FileDownload / File: emd_76459.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.752 Å		0.82 Å/pix.
x 320 pix.
= 262.752 Å		0.82 Å/pix.
x 320 pix.
= 262.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8211 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.054
Minimum - Maximum-0.07729671 - 0.34191546
Average (Standard dev.)0.00081937213 (±0.009402223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.752 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76459_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_76459_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76459_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76459_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : [NiFe]-hydrogenase HoxEFU diaphorase subcomplex

EntireName: [NiFe]-hydrogenase HoxEFU diaphorase subcomplex
Components
  • Complex: [NiFe]-hydrogenase HoxEFU diaphorase subcomplex
    • Complex: [NiFe]-hydrogenase HoxE subunit
      • Protein or peptide: [NiFe]-hydrogenase HoxE subunit
    • Complex: [NiFe]-hydrogenase HoxF subunit
      • Protein or peptide: [NiFe]-hydrogenase HoxF subunit
    • Complex: [NiFe]-hydrogenase HoxU subunit
      • Protein or peptide: [NiFe]-hydrogenase HoxU subunit

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Supramolecule #1: [NiFe]-hydrogenase HoxEFU diaphorase subcomplex

SupramoleculeName: [NiFe]-hydrogenase HoxEFU diaphorase subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: [NiFe]-hydrogenase HoxE subunit

SupramoleculeName: [NiFe]-hydrogenase HoxE subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Supramolecule #3: [NiFe]-hydrogenase HoxF subunit

SupramoleculeName: [NiFe]-hydrogenase HoxF subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Supramolecule #4: [NiFe]-hydrogenase HoxU subunit

SupramoleculeName: [NiFe]-hydrogenase HoxU subunit / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: [NiFe]-hydrogenase HoxE subunit

MacromoleculeName: [NiFe]-hydrogenase HoxE subunit / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTVATDRQTV PPSAAHPSGD KRFKVLDATM KRNQFNQDAL IEILHKAQEI FGYLEEDVLL YVARGLKLPL SRVFGVATFY HLFSLKPSGK HTCVVCLGTA CYVKGAGDLL KTLDQEVHLK PGETTEDGQM SLVTARCIGA CGIAPAVVYD GKVLGKQNDE AVLAAIQPWL SNS

UniProtKB: Potential NAD-reducing hydrogenase subunit

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Macromolecule #2: [NiFe]-hydrogenase HoxF subunit

MacromoleculeName: [NiFe]-hydrogenase HoxF subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDIKELKEIA TKSREKQTKI RIRCCSAAGC LSSEGETVKK NLTTAIAAAG LEEKVEVCGV GCMKFCGRGP LVAVDDRNQL YEFVTPDQVG DIVKKLQKPD AVAETGLISG DPHHPFYALQ RNIALENSGR IDPESIDEYI ALGGYEQLHK VVYEMTPEEV IVEMNKSGLR ...String:
MDIKELKEIA TKSREKQTKI RIRCCSAAGC LSSEGETVKK NLTTAIAAAG LEEKVEVCGV GCMKFCGRGP LVAVDDRNQL YEFVTPDQVG DIVKKLQKPD AVAETGLISG DPHHPFYALQ RNIALENSGR IDPESIDEYI ALGGYEQLHK VVYEMTPEEV IVEMNKSGLR GRGGGGYPTG LKWATVAKMP GQQKYVICNA DEGDPGAFMD RSVLESDPHR ILEGMAIAAY AVGANHGYIY VRAEYPLAIQ RLQKAIQQAK RYGLMGTQIF DSPIDFKIDI RVGAGAFVCG EETALIASVE GKRGTPRPR PPYPAQSGLW QSPTLINNVE TYANVVPIIR EGGDWYGSIG TEKSKGTKVF ALTGKVENAG LIEVPMGTTV RQVVEEMGGG VPNGGQVKAV QTGGPSGGCI PADKLDTPIE YDTLLALGTM MGSGGMIVMD ESTNMVDVAQ FYMDFCKSES CGKCIPCRAG TVQLYDLLTR FLEGEATQED LIKLENLCHM VKETSLCGLG MSAPNPVIST LRYFRHEYEE LLKV

UniProtKB: Hydrogenase subunit

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Macromolecule #3: [NiFe]-hydrogenase HoxU subunit

MacromoleculeName: [NiFe]-hydrogenase HoxU subunit / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSVVTLTIDD KAIAIEEGAS ILQAAKEAGV PIPTLCHLEG ISEAAACRLC MVEVEGTNKL MPACVTAVSE EMVVHTNTEK LQNYRRMTVE LLFSEGNHVC AICVANGNCE LQDMAITVGM DHSRFKYQFP KREVDLSHPM FGIDHNRCIL CTRCVRVCDE IEGAHVWDVA ...String:
MSVVTLTIDD KAIAIEEGAS ILQAAKEAGV PIPTLCHLEG ISEAAACRLC MVEVEGTNKL MPACVTAVSE EMVVHTNTEK LQNYRRMTVE LLFSEGNHVC AICVANGNCE LQDMAITVGM DHSRFKYQFP KREVDLSHPM FGIDHNRCIL CTRCVRVCDE IEGAHVWDVA YRGAECKIVS GLNQPWGTVD ACTSCGKCVD ACPTGSIFHK GETTAEKIGD RRKVEFLATA RKEKEWVR

UniProtKB: Hydrogenase subunit

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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

Concentration0.4 mg/mL
BufferpH: 8.3
Component:
ConcentrationFormulaName
50.0 mMTrisTris
300.0 mMNaClSodium Chloride
5.0 %GlycerolGlycerol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3
Details: Grids were blotted for 3.0 seconds before plunging into liquid ethane..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3694 / 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 882000
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 52000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 200 / Avg.num./class: 4000 / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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