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- PDB-3zfs: Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a me... -

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Basic information

Entry
Database: PDB / ID: 3zfs
TitleCryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate
Components(F420-REDUCING HYDROGENASE, SUBUNIT ...) x 3
KeywordsOXIDOREDUCTASE / METHANOGENESIS
Function / homology
Function and homology information


coenzyme F420 hydrogenase / coenzyme F420 hydrogenase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Coenzyme F420 hydrogenase, subunit alpha / Coenzyme F420 hydrogenase subunit beta, archaea / Coenzyme F420 hydrogenase, subunit gamma / : / 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 / Nickel-dependent hydrogenases large subunit signature 2. ...Coenzyme F420 hydrogenase, subunit alpha / Coenzyme F420 hydrogenase subunit beta, archaea / Coenzyme F420 hydrogenase, subunit gamma / : / 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 / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / 4Fe-4S binding domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 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
Similarity search - Domain/homology
COENZYME F420 / FLAVIN-ADENINE DINUCLEOTIDE / CARBONMONOXIDE-(DICYANO) IRON / : / NICKEL (II) ION / IRON/SULFUR CLUSTER / Coenzyme F420 hydrogenase subunit beta / Coenzyme F420 hydrogenase subunit gamma / Coenzyme F420 hydrogenase subunit alpha
Similarity search - Component
Biological speciesMETHANOTHERMOBACTER MARBURGENSIS (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C
AuthorsMills, D.J. / Vitt, S. / Strauss, M. / Shima, S. / Vonck, J.
CitationJournal: Elife / Year: 2013
Title: De novo modeling of the F(420)-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy.
Authors: Deryck J Mills / Stella Vitt / Mike Strauss / Seigo Shima / Janet Vonck /
Abstract: Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the ...Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure. DOI:http://dx.doi.org/10.7554/eLife.00218.001.
History
DepositionDec 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Assembly

Deposited unit
A: F420-REDUCING HYDROGENASE, SUBUNIT ALPHA
B: F420-REDUCING HYDROGENASE, SUBUNIT GAMMA
C: F420-REDUCING HYDROGENASE, SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,13612
Polymers105,9203
Non-polymers3,2169
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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F420-REDUCING HYDROGENASE, SUBUNIT ... , 3 types, 3 molecules ABC

#1: Protein F420-REDUCING HYDROGENASE, SUBUNIT ALPHA / FRHA / COENZYME F420 HYDROGENASE ALPHA SUBUNIT / Coordinate model: Cα atoms only


Mass: 44873.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FRHA CONTAINS A NIFE CENTER
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
Strain: DSM 2133 / References: UniProt: D9PYF9, coenzyme F420 hydrogenase
#2: Protein F420-REDUCING HYDROGENASE, SUBUNIT GAMMA / FRHG / COENZYME F420 HYDROGENASE GAMMA SUBUNIT / Coordinate model: Cα atoms only


Mass: 30267.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FRHG CONTAINS THREE 4FE4S CLUSTERS
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
Strain: DSM 2133 / References: UniProt: D9PYF7, coenzyme F420 hydrogenase
#3: Protein F420-REDUCING HYDROGENASE, SUBUNIT BETA / FRHB / COENZYME F420 HYDROGENASE BETA SUBUNIT / Coordinate model: Cα atoms only


Mass: 30778.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FRHB CONTAINS FAD AND A 4FE4S CLUSTER
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
Strain: DSM 2133 / References: UniProt: D9PYF6, coenzyme F420 hydrogenase

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Non-polymers , 6 types, 9 molecules

#4: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N5O18P
#9: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

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Details

Nonpolymer detailsCOENZYME F420 (F42): ONLY ISOALLOXAZINE RING CARBONMONOXIDE-(DICYANO) IRON (FCO): ONLY FE ION

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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-REDUCING HYDROGENASE / Type: COMPLEX
Buffer solutionName: 50 MM TRIS/HCL, 2 MM DTT, 0.025 MM FAD / pH: 7.6 / Details: 50 MM TRIS/HCL, 2 MM DTT, 0.025 MM FAD
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Feb 11, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 61400 X / Nominal defocus max: 3820 nm / Nominal defocus min: 1650 nm / Cs: 2 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 80
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3EMAN23D reconstruction
CTF correctionDetails: PER MICROGRAPH
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionMethod: REFINEMENT IN EMAN2 / Resolution: 4 Å / Num. of particles: 97290 / Nominal pixel size: 1.19 Å / Actual pixel size: 1.14 Å / Magnification calibration: FIT OF X-RAY MODEL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2097.(DEPOSITION ID: 10788).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model buildingPDB-ID: 2WPN

2wpn


Accession code: 2WPN / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4 Å
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 107 0 985

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