[English] 日本語
Yorodumi
- PDB-5vkv: Solution NMR structure of the membrane electron transporter CcdA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vkv
TitleSolution NMR structure of the membrane electron transporter CcdA
ComponentsCytochrome c-type biogenesis protein CcdA
KeywordsOXIDOREDUCTASE / Membrane transporter / DsbD
Function / homology: / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / cytochrome complex assembly / membrane / Cytochrome c-type biogenesis protein CcdA
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZhou, Y. / Bushweller, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM078296 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Solution structure and elevator mechanism of the membrane electron transporter CcdA.
Authors: Zhou, Y. / Bushweller, J.H.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c-type biogenesis protein CcdA


Theoretical massNumber of molelcules
Total (without water)25,2921
Polymers25,2921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average and lowest energy

-
Components

#1: Protein Cytochrome c-type biogenesis protein CcdA


Mass: 25292.143 Da / Num. of mol.: 1 / Mutation: E35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1409 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SIG0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
122isotropic12D 1H-15N HSQC
132isotropic13D HNCA
142isotropic13D HN(CO)CA
152isotropic13D HNCO
162isotropic13D HN(CA)CO
172isotropic13D HN(CA)CB
182isotropic13D 1H-15N NOESY
193anisotropic12D 1H-15N HSQC
1104anisotropic12D 1H-15N HSQC
1115isotropic12D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle20.37 mM [U-13C; U-15N; U-2H] CcdA, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2Ofor assignment and NOEs2H,13C,15N_sample90% H2O/10% D2O
micelle30.7 mM [U-15N; U-2H] CcdA, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O3.8% (w/v) polyacrylamide gel, stretched from 6.0mm diameter to 4.24mm diameterRDC_neutral_gel_sample90% H2O/10% D2O
micelle40.7 mM [U-15N; U-2H] CcdA, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O2.0%(w/v) polyacrylamide and 2.0% (3-acrylamidopropyl)-trimethylammonium chloride, vertically pressed from 21mm to 16mmRDC_positive_gel_sample90% H2O/10% D2O
micelle50.2 mM [U-15N] CcdA single Cys mutants labeled with MTSL, 25 mM sodium acetate, 25 mM potassium phosphate, 50 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2OPRE_samples90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.37 mMCcdA[U-13C; U-15N; U-2H]2
25 mMsodium acetatenatural abundance2
25 mMpotassium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
0.05 %sodium azidenatural abundance2
0.7 mMCcdA[U-15N; U-2H]3
25 mMsodium acetatenatural abundance3
25 mMpotassium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
0.05 %sodium azidenatural abundance3
0.7 mMCcdA[U-15N; U-2H]4
25 mMsodium acetatenatural abundance4
25 mMpotassium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
0.05 %sodium azidenatural abundance4
0.2 mMCcdA single Cys mutants labeled with MTSL[U-15N]5
25 mMsodium acetatenatural abundance5
25 mMpotassium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
0.05 %sodium azidenatural abundance5
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 343 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.39Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.39Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Analysis2.4.2CCPNchemical shift assignment
Analysis2.4.2CCPNpeak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS-NYang Shen, and Ad Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average and lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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