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- PDB-2l0y: Complex hMia40-hCox17 -

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Basic information

Entry
Database: PDB / ID: 2l0y
TitleComplex hMia40-hCox17
Components
  • COX17 cytochrome c oxidase assembly homolog (S. cerevisiae) pseudogene (COX17)
  • Mitochondrial intermembrane space import and assembly protein 40
KeywordsPROTEIN TRANSPORT/METAL TRANSPORT / Oxidative Protein Folding / Macromolecular complex / Mitochondrial Import / PROTEIN TRANSPORT-METAL TRANSPORT complex
Function / homology
Function and homology information


'de novo' post-translational protein folding / positive regulation of cytochrome-c oxidase activity / peptidyl-cysteine oxidation / Complex IV assembly / copper chaperone activity / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / positive regulation of cellular respiration / mitochondrial cytochrome c oxidase assembly / copper ion transport ...'de novo' post-translational protein folding / positive regulation of cytochrome-c oxidase activity / peptidyl-cysteine oxidation / Complex IV assembly / copper chaperone activity / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / positive regulation of cellular respiration / mitochondrial cytochrome c oxidase assembly / copper ion transport / Mitochondrial protein import / regulation of protein export from nucleus / protein maturation by protein folding / mitochondrial DNA repair / cuprous ion binding / protein-disulfide reductase activity / enzyme activator activity / cellular response to leukemia inhibitory factor / generation of precursor metabolites and energy / mitochondrial intermembrane space / cellular response to oxidative stress / copper ion binding / positive regulation of cell population proliferation / mitochondrion / cytoplasm
Similarity search - Function
Helix Hairpins - #2900 / Mitochondrial intermembrane space import and assembly protein 40 / Cytochrome c oxidase copper chaperone / Cytochrome C oxidase copper chaperone (COX17) / Cysteine alpha-hairpin motif superfamily / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytochrome c oxidase copper chaperone / : / Mitochondrial intermembrane space import and assembly protein 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsBertini, I. / Ciofi-Baffoni, S. / Gallo, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Molecular chaperone function of Mia40 triggers consecutive induced folding steps of the substrate in mitochondrial protein import.
Authors: Banci, L. / Bertini, I. / Cefaro, C. / Cenacchi, L. / Ciofi-Baffoni, S. / Felli, I.C. / Gallo, A. / Gonnelli, L. / Luchinat, E. / Sideris, D. / Tokatlidis, K.
History
DepositionJul 20, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: 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: _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial intermembrane space import and assembly protein 40
B: COX17 cytochrome c oxidase assembly homolog (S. cerevisiae) pseudogene (COX17)


Theoretical massNumber of molelcules
Total (without water)23,7662
Polymers23,7662
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 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitochondrial intermembrane space import and assembly protein 40 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 4


Mass: 16387.693 Da / Num. of mol.: 1 / Mutation: C53S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHCHD4, MIA40 / Plasmid: pDEST-His-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N4Q1
#2: Protein COX17 cytochrome c oxidase assembly homolog (S. cerevisiae) pseudogene (COX17) / HCG2020266


Mass: 7378.574 Da / Num. of mol.: 1 / Mutation: C26S C36S C55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_2020266, RP11-189B4.3-001 / Plasmid: pETG-30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5W0Q5, UniProt: Q14061*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1312D 1H-1H NOESY
1422D 1H-1H NOESY
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HN(CO)CA
11023D HNCO
11123D HNCA
11223D HN(CA)CB
11323D CBCA(CO)NH
11423D HN(CO)CA
11513D 1H-15N NOESY
11613D 1H-13C NOESY
11723D 1H-15N NOESY
11823D 1H-13C NOESY
11913D ω1- 13C-edited, ω2-13C-filtered NOESY
12023D ω1- 13C-edited, ω2-13C-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] Mia40, 0.5 mM Cox17, 50 mM Phosphate, 0.5 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] Cox17, 0.5 mM Mia40, 50 mM Phosphate, 0.5 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMia40-1[U-100% 13C; U-100% 15N]1
0.5 mMCox17-21
50 mMPhosphate-31
0.5 mMEDTA-41
0.5 mMCox17-5[U-100% 13C; U-100% 15N]2
0.5 mMMia40-62
50 mMPhosphate-72
0.5 mMEDTA-82
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA2Keller and Wuthrichchemical shift assignment
CARA2Keller and Wuthrichdata analysis
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1 / Details: AMBER 10.0, AMBER 10.0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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