[English] 日本語
Yorodumi
- PDB-1s3a: NMR Solution Structure of Subunit B8 from Human NADH-Ubiquinone O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s3a
TitleNMR Solution Structure of Subunit B8 from Human NADH-Ubiquinone Oxidoreductase Complex I (CI-B8)
ComponentsNADH-ubiquinone oxidoreductase B8 subunit
KeywordsOXIDOREDUCTASE / CI-B8 / NDUFA2 / Complex I
Function / homology
Function and homology information


Complex I biogenesis / blastocyst hatching / Respiratory electron transport / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / aerobic respiration / mitochondrial membrane / mitochondrial inner membrane
Similarity search - Function
NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated anealing
AuthorsBrockmann, C. / Diehl, A. / Rehbein, K. / Kuhne, R. / Oschkinat, H.
CitationJournal: Structure / Year: 2004
Title: The oxidized subunit B8 from human complex I adopts a thioredoxin fold.
Authors: Brockmann, C. / Diehl, A. / Rehbein, K. / Strauss, H. / Schmieder, P. / Korn, B. / Kuhne, R. / Oschkinat, H.
History
DepositionJan 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase B8 subunit


Theoretical massNumber of molelcules
Total (without water)11,1951
Polymers11,1951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein NADH-ubiquinone oxidoreductase B8 subunit / Complex I-B8 / CI-B8


Mass: 11194.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDUFA2 / Plasmid: pDEST17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O43678, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1233D 13C-separated NOESY
1332D NOESY
1423D 13C-separated NOESY
1533D 13C methyl selective NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N, 90% H2O, 10% D2O90% H2O/10% D2O
2U-15N, U-13C, 90% H2O, 10% D2O90% H2O/10% D2O
3U-15N, U-13C, 100% D2O100% D2O
Sample conditionsIonic strength: 20mM phosphate, 50mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
Sparky3.1T.D.Goddard and D.G.Knellerdata analysis
CYANAGunther, T.data analysis
CNS1Brunger, A.refinement
RefinementMethod: simulated anealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 19

+
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