[English] 日本語
Yorodumi
- PDB-1u97: Solution Structure of Apo Yeast Cox17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u97
TitleSolution Structure of Apo Yeast Cox17
ComponentsCytochrome c oxidase copper chaperone
KeywordsCHAPERONE / Metallochaperone / Unstructured N-terminus / Two Alpha-Helices / Cytochrome c Oxidase
Function / homology
Function and homology information


protein maturation by copper ion transfer / copper chaperone activity / protein farnesylation / mitochondrial cytochrome c oxidase assembly / cuprous ion binding / mitochondrial intermembrane space / mitochondrion / cytosol
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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsAbajian, C. / Yatsunyk, L.A. / Ramirez, B.E. / Rosenzweig, A.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Yeast cox17 solution structure and Copper(I) binding.
Authors: Abajian, C. / Yatsunyk, L.A. / Ramirez, B.E. / Rosenzweig, A.C.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c oxidase copper chaperone


Theoretical massNumber of molelcules
Total (without water)8,0691
Polymers8,0691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80lowest retraint energies, restraint violations, and RMS deviations from ideal
RepresentativeModel #1closest to the average

-
Components

#1: Protein Cytochrome c oxidase copper chaperone


Mass: 8069.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: COX17 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q12287

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited NOESY
1213D 13C-edited NOESY
NMR detailsText: nmr samples were reduced and kept anaerobic

-
Sample preparation

DetailsContents: 1mM Cox17 U-15N,13C; 20mM Potassium Phosphate, pH 6.0
Solvent system: H2O/D2O
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger et al.structure solution
ARIA1.2Linge and Nilgesstructure solution
Felix2000Accelrys Inc.processing
VNMR6.1BVarian Assoc. Inc.collection
ARIA1.2Linge and Nilgesrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest retraint energies, restraint violations, and RMS deviations from ideal
Conformers calculated total number: 80 / 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