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- PDB-8rvu: CryoEM structure of the Elp-Hdr complex of Methanothermobacter ma... -

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Basic information

Entry
Database: PDB / ID: 8rvu
TitleCryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2 (composite structure)
Components
  • (Formate dehydrogenase, ...) x 2
  • (H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit ...) x 3
  • Methyl viologen-reducing hydrogenase, subunit D-related protein
KeywordsOXIDOREDUCTASE / Redox / Flavin-based electron bifurcation / methanogenesis / heterodisulfide reductase / F420-H2 oxidase
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
Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsSan Segundo-Acosta, P. / Murphy, B.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Altered electron flow in hydrogenotrophic methanogens under nickel limitation
Authors: Nomura, S. / San Segundo-Acosta, P. / Kahnt, J. / Murphy, B.J. / Shima, S.
History
DepositionFeb 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Formate dehydrogenase, beta subunit
D: Formate dehydrogenase, alpha subunit
F: Methyl viologen-reducing hydrogenase, subunit D-related protein
b: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
B: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
c: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
C: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
a: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
A: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,50935
Polymers349,2419
Non-polymers10,26926
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Formate dehydrogenase, ... , 2 types, 2 molecules ED

#1: Protein Formate dehydrogenase, beta subunit


Mass: 43387.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: D9PY03, formate dehydrogenase
#2: Protein Formate dehydrogenase, alpha subunit


Mass: 37682.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: D9PY04, formate dehydrogenase

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Protein , 1 types, 1 molecules F

#3: Protein Methyl viologen-reducing hydrogenase, subunit D-related protein


Mass: 15550.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: D9PY02

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H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit ... , 3 types, 6 molecules bBcCaA

#4: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / CoB--CoM heterodisulfide reductase subunit B


Mass: 33496.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50755, H2:CoB-CoM heterodisulfide,ferredoxin reductase
#5: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / CoB--CoM heterodisulfide reductase iron-sulfur subunit C


Mass: 20548.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50754, H2:CoB-CoM heterodisulfide,ferredoxin reductase
#6: Protein H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A / CoB--CoM heterodisulfide reductase iron-sulfur subunit A


Mass: 72264.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50756, H2:CoB-CoM heterodisulfide,ferredoxin reductase

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Non-polymers , 5 types, 197 molecules

#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#9: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 0.45 MDa / Experimental value: NO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Buffer solutionpH: 7.6
Details: 50 mM Tris-HCl pH 7.6 containing 400 mM Ammonium sulfate.
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7768
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
13RELIONclassification
14cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234858 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Automated model building using model angelo / Source name: Other / Type: other
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222921
ELECTRON MICROSCOPYf_angle_d0.54431152
ELECTRON MICROSCOPYf_dihedral_angle_d5.5143288
ELECTRON MICROSCOPYf_chiral_restr0.0423465
ELECTRON MICROSCOPYf_plane_restr0.0044000

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