[English] 日本語
Yorodumi
- PDB-2rn9: Solution structure of human apoCox17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rn9
TitleSolution structure of human apoCox17
ComponentsCytochrome c oxidase copper chaperone
KeywordsMETAL TRANSPORT / coiled coil-helix-coiled coil-helix domain / copper binding protein / alpha-hairpin fold / Chaperone / Metal-binding / Mitochondrion
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 / simulated annealing
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Janicka, A. / Martinelli, M. / Kozlowski, H. / Palumaa, P.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A structural-dynamical characterization of human cox17
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Janicka, A. / Martinelli, M. / Kozlowski, H. / Palumaa, P.
History
DepositionDec 8, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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 oxidase copper chaperone


Theoretical massNumber of molelcules
Total (without water)7,3211
Polymers7,3211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein Cytochrome c oxidase copper chaperone / Cox17


Mass: 7320.556 Da / Num. of mol.: 1
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
1122D 1H-15N HSQC
1233D CBCA(CO)NH
1333D HN(CA)CB
1433D HNCA
1533D HNCO
1633D HN(CO)CA
1733D HBHA(CO)NH
1833D (H)CCH-TOCSY
1912D 1H-1H NOESY
11023D 1H-15N NOESY
11133D 1H-13C NOESY
11212D 1H-1H TOCSY
11323D HNHA
11433D HN(CA)CO

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1mM Cox17; 1mM DTT; 50mM potassium phosphate; 90% H2O/10% D2O90% H2O/10% D2O
20.5-1mM [U-100% 15N] Cox17; 1mM DTT; 50mM potassium phosphate; 90% H2O/10% D2O90% H2O/10% D2O
30.5-1mM [U-100% 13C; U-100% 15N] Cox17; 1mM DTT; 50mM potassium phosphate; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCox171
1 mMDTT1
50 mMpotassium phosphate1
0.5 mMCox17[U-100% 15N]2
1 mMDTT2
50 mMpotassium phosphate2
0.5 mMCox17[U-100% 13C; U-100% 15N]3
1 mMDTT3
50 mMpotassium phosphate3
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
Bruker AvanceBrukerAVANCE7003

-
Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollrefinement
TopSpinBruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ATNOSHerrmann, Guntert, Wuthrichpeak picking
CANDIDHerrmann, Guntert, Wuthrichnoes assignment
CARAKellerdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NMR refinement is based on NOE-derived distance restraints and torsion angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / 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