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- PDB-1z2g: Solution structure of apo, oxidized yeast Cox17 -

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Basic information

Entry
Database: PDB / ID: 1z2g
TitleSolution structure of apo, oxidized yeast Cox17
ComponentsCytochrome c oxidase copper chaperone
KeywordsCHAPERONE / Copper Chaperone / Cytochrome c Oxidase assembly / disulfide bonds / coiled coil-helix-coiled coil-helix domain / Structural Genomics / Structural Proteomics in Europe / SPINE
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 / simulated annealing, torsion angle dynamics
Model type detailsminimized average
AuthorsArnesano, F. / Balatri, E. / Banci, L. / Bertini, I. / Winge, D.R. / Structural Proteomics in Europe (SPINE)
CitationJournal: STRUCTURE / Year: 2005
Title: Folding studies of Cox17 reveal an important interplay of cysteine oxidation and copper binding
Authors: Arnesano, F. / Balatri, E. / Banci, L. / Bertini, I. / Winge, D.R.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c oxidase copper chaperone


Theoretical massNumber of molelcules
Total (without water)8,0691
Polymers8,0691
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)1 / -
Representativeminimized average structure

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Components

#1: Protein Cytochrome c oxidase copper chaperone / Cox17


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: YLL009C / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12287

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
141HNHA
1512D TOCSY

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Sample preparation

DetailsContents: 2mM Cox17 15N, 13C; 1mM dithiothreitol; 50mM phosphate buffer; pH 7
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRprocessing
XEASYdata analysis
DYANAGuentert, Mumenthaler and Wuethrichstructure solution
Amber6refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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