[English] 日本語
Yorodumi
- PDB-7e5z: Dehydrogenase holoenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e5z
TitleDehydrogenase holoenzyme
Components
  • Formate dehydrogenase
  • Tungsten-containing formate dehydrogenase beta subunit
KeywordsOXIDOREDUCTASE / Formate dehydrogenase / ELECTRON TRANSPORT
Function / homology
Function and homology information


formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding ...formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Formate dehydrogenase H, molybdopterin-binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain ...Formate dehydrogenase H, molybdopterin-binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB domain / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Aspartate decarboxylase-like domain superfamily / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S dicluster 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
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-MGD / IRON/SULFUR CLUSTER / : / Tungsten-containing formate dehydrogenase beta subunit / formate dehydrogenase
Similarity search - Component
Biological speciesMethylorubrum extorquens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRoh, S.H. / Park, J.S. / Heo, Y.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015M3D3A1A01064919 Korea, Republic Of
CitationJournal: To Be Published
Title: Dehydrogenase holoenzyme
Authors: Roh, S.H. / Park, J.S.
History
DepositionFeb 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Structure summary / Category: audit_author / citation / struct
Item: _audit_author.identifier_ORCID / _citation.title / _struct.title

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30995
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formate dehydrogenase
B: Tungsten-containing formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,57012
Polymers170,6902
Non-polymers3,87910
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9330 Å2
ΔGint-174 kcal/mol
Surface area53970 Å2

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Formate dehydrogenase /


Mass: 108292.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: fdh1A, MexAM1_META1p5032 / Production host: Methylorubrum extorquens AM1 (bacteria) / References: UniProt: C5ATT7, formate dehydrogenase
#2: Protein Tungsten-containing formate dehydrogenase beta subunit


Mass: 62397.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: fdh1B, MexAM1_META1p5031 / Production host: Methylorubrum extorquens AM1 (bacteria) / References: UniProt: C5ATT6, formate dehydrogenase

-
Non-polymers , 5 types, 10 molecules

#3: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W
#4: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1)COMPLEX#1-#20RECOMBINANT
2Formate dehydrogenase alpha subunit from Methylobacterium extorquens AM1 (MeFDH1)COMPLEX#11RECOMBINANT
3Formate dehydrogenase beta subunit from Methylobacterium extorquens AM1 (MeFDH1)COMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.16 MDaYES
210.1 MDaYES
310.07 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Methylorubrum extorquens AM1 (bacteria)272630
32Methylorubrum extorquens AM1 (bacteria)272630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Methylorubrum extorquens AM1 (bacteria)272630
32Methylorubrum extorquens AM1 (bacteria)272630
Buffer solutionpH: 6.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium phosphateNa2HPO41
2100 mMsodium chlorideNaclSodium chloride1
32 mMDithiothreitolC4H10O2S21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K
Details: Blot time was for 4 seconds with 0 blot force before plunging.

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 100000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 350 mradians
Image recordingAverage exposure time: 3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2683 / Details: Images were collected in movie-mode at
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
7ISOLDE1.0.1model fittingISODE was plugged in UCSF ChimeraX
8UCSF Chimera1.13.1model fitting
10cryoSPARC2.15.0initial Euler assignment
11cryoSPARC2.15.0final Euler assignment
13cryoSPARC2.15.03D reconstruction
14PHENIX1.19.1model refinement
15Coot0.8.9.2model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1471548 / Details: Topaz picking facilitated particle picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260910 / Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Details: A initial model was from SWISS modeling using 6TGA as a template. Initial local fitting was done using Chimera and then ISOLDE plugged in ChimeraX for flexible fitting. The model was refined ...Details: A initial model was from SWISS modeling using 6TGA as a template. Initial local fitting was done using Chimera and then ISOLDE plugged in ChimeraX for flexible fitting. The model was refined by using Phenix and Coot.
Atomic model buildingPDB-ID: 6TGA

6tga

RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 90.64 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.032210494
ELECTRON MICROSCOPYf_angle_d0.849814303
ELECTRON MICROSCOPYf_chiral_restr0.17081573
ELECTRON MICROSCOPYf_plane_restr0.00431865
ELECTRON MICROSCOPYf_dihedral_angle_d20.70356187

+
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