[English] 日本語
Yorodumi
- PDB-3zfs: Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a me... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 4Fe-4S dicluster domain / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / 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 / 4Fe-4S dicluster domain / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / 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 / F420-reducing hydrogenase, subunit beta / F420-reducing hydrogenase, subunit gamma / F420-reducing 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-2096
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-2097
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2096
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-2096
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-2097
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-2097
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
1


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

-
Components

-
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

-
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 / Nickel


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 / Iron–sulfur cluster


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


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


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

-
Details

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

-
Experimental details

-
Experiment

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

-
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

-
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 FIELDBright-field microscopy / 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

-
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

RefinementHighest resolution: 4 Å
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 107 0 985

+
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