[English] 日本語
Yorodumi
- PDB-2lgq: Human C30S/C59S-Cox17 mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lgq
TitleHuman C30S/C59S-Cox17 mutant
ComponentsCytochrome c oxidase copper chaperone
KeywordsMETAL TRANSPORT / Mitochondrial protein / Copper chaperone / IMS / cytochrome c oxidase
Function / homology
Function and homology information


positive regulation of cytochrome-c oxidase activity / copper chaperone activity / mitochondrial cytochrome c oxidase assembly / copper ion transport / Mitochondrial protein import / ion binding / cuprous ion binding / enzyme activator activity / generation of precursor metabolites and energy / mitochondrial intermembrane space ...positive regulation of cytochrome-c oxidase activity / copper chaperone activity / mitochondrial cytochrome c oxidase assembly / copper ion transport / Mitochondrial protein import / ion binding / cuprous ion binding / enzyme activator activity / generation of precursor metabolites and energy / mitochondrial intermembrane space / copper ion binding / positive regulation of cell population proliferation / cytoplasm
Similarity search - Function
Cytochrome c oxidase copper chaperone / Cytochrome C oxidase copper chaperone (COX17) / CytochromE C oxidase copper chaperone / Cysteine alpha-hairpin motif superfamily / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytochrome c oxidase copper chaperone
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsBertini, I. / Ciofi-Baffoni, S. / Gallo, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Functional role of two interhelical disulfide bonds in human cox17 protein from a structural perspective.
Authors: Banci, L. / Bertini, I. / Cefaro, C. / Ciofi-Baffoni, S. / Gallo, A.
History
DepositionAug 1, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c oxidase copper chaperone


Theoretical massNumber of molelcules
Total (without water)7,2881
Polymers7,2881
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)20 / 400target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Cytochrome c oxidase copper chaperone


Mass: 7288.426 Da / Num. of mol.: 1 / Mutation: C30S, C59S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COX17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Origami(DE3) / References: UniProt: Q14061

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HN(CA)CB
1423D HNCA
1523D HN(CO)CA
1623D HNCO
1723D HBHA(CO)NH
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11112D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] protein, 50 mM sodium phosphate, 0.5 mM EDTA, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] protein, 50 mM sodium phosphate, 0.5 mM EDTA, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-100% 15N]1
50 mMsodium phosphate-21
0.5 mMEDTA-31
1 mMDTT-41
1 mMentity-5[U-99% 13C; U-99% 15N]2
50 mMsodium phosphate-62
0.5 mMEDTA-72
1 mMDTT-82
Sample conditionsIonic strength: 50 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE5002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospindata analysis
TopSpin2.1Bruker Biospinprocessing
CARA2.1Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
PECANEghbalnia, Wang, Bahrami, Assadi, and Markleydata analysis
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 537 / NOE intraresidue total count: 158 / NOE long range total count: 24 / NOE medium range total count: 206 / NOE sequential total count: 149 / Protein phi angle constraints total count: 46 / Protein psi angle constraints total count: 46
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

+
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