[English] 日本語
Yorodumi
- PDB-4ci0: Electron cryo-microscopy of F420-reducing NiFe hydrogenase Frh -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ci0
TitleElectron cryo-microscopy of F420-reducing NiFe hydrogenase Frh
Components(F420-REDUCING HYDROGENASE, SUBUNIT ...) x 3
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / ELECTRON TRANSFER / FERREDOXIN
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
Nuclear Transport Factor 2; Chain: A, - #750 / 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 ...Nuclear Transport Factor 2; Chain: A, - #750 / 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 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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 / Alpha-Beta Plaits - #20 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Nuclear Transport Factor 2; Chain: A, / 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 / Alpha-Beta Plaits / Roll / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / : / 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: 3.36 Å
AuthorsAllegretti, M. / Mills, D.J. / McMullan, G. / Kuehlbrandt, W. / Vonck, J.
CitationJournal: Elife / Year: 2014
Title: Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.
Authors: Matteo Allegretti / Deryck J Mills / Greg McMullan / Werner Kühlbrandt / Janet Vonck /
Abstract: The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct ...The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes. DOI: http://dx.doi.org/10.7554/eLife.01963.001.
History
DepositionDec 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Movie
  • Biological unit as complete point assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2513
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-2513
  • 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)106,17112
Polymers103,7433
Non-polymers2,4289
Water00
1
A: F420-REDUCING HYDROGENASE, SUBUNIT ALPHA
B: F420-REDUCING HYDROGENASE, SUBUNIT GAMMA
C: F420-REDUCING HYDROGENASE, SUBUNIT BETA
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,274,054144
Polymers1,244,91936
Non-polymers29,135108
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: T (tetrahedral))

-
Components

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

#1: Protein F420-REDUCING HYDROGENASE, SUBUNIT ALPHA / F420 REDUCING NIFE HYDROGENASE


Mass: 42696.773 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-386 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
References: UniProt: D9PYF9, coenzyme F420 hydrogenase
#2: Protein F420-REDUCING HYDROGENASE, SUBUNIT GAMMA / F420 REDUCING NIFE HYDROGENASE


Mass: 30267.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
References: UniProt: D9PYF7, coenzyme F420 hydrogenase
#3: Protein F420-REDUCING HYDROGENASE, SUBUNIT BETA / F420 REDUCING NIFE HYDROGENASE


Mass: 30778.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
References: UniProt: D9PYF6, coenzyme F420 hydrogenase

-
Non-polymers , 6 types, 9 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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

-
Details

Has protein modificationY
Nonpolymer detailsZINC ION (ZN): A ZINC ION IS SHARED BY TWO FRHG SUBUNITS
Sequence detailsTHE SEQUENCE AFTER HIS386 HAS BEEN REMOVED BY AN ENDOPEPTIDASE IN CHAIN A

-
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: 50MM TRIS-HCL, 0.025MM FAD / pH: 7.6 / Details: 50MM TRIS-HCL, 0.025MM 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: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 103, INSTRUMENT- FEI VITROBOT MARK I, METHOD- BLOTTING 2.5 SECONDS BEFORE PLUNGING,

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: May 27, 2013 / Details: DATA WAS COLLECTED IN MOVIE MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 78000 X / Calibrated magnification: 106000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.2 mm
Specimen holderTemperature: 79 K
Image recordingElectron dose: 22 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 235
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1Cootmodel fitting
2RELION3D reconstruction
CTF correctionDetails: EACH IMAGE
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionMethod: MAXIMUM LIKELIHOOD / Resolution: 3.36 Å / Num. of particles: 26000 / Nominal pixel size: 1.32 Å / Actual pixel size: 1.32 Å / Magnification calibration: FIT TO ATOMIC MODEL
Details: FRH IS A FRHABG DODECAMER WITH TETRAHEDRAL SYMMETRY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2513. (DEPOSITION ID: 12073).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--CRYO-EM
Atomic model buildingPDB-ID: 3ZFS

3zfs


Accession code: 3ZFS / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.36 Å
Refinement stepCycle: LAST / Highest resolution: 3.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6867 0 89 0 6956

+
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