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- PDB-2k3j: The solution structure of human Mia40 -

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Basic information

Entry
Database: PDB / ID: 2k3j
TitleThe solution structure of human Mia40
ComponentsMitochondrial intermembrane space import and assembly protein 40
KeywordsOXIDOREDUCTASE / alpha-hairpin fold / COILED COIL-HELIX-COILED COIL-HELIX DOMAIN / Mitochondrial oxidase / Protein import and folding / Alternative splicing / Mitochondrion / Protein transport / Translocation / Transport
Function / homology
Function and homology information


'de novo' post-translational protein folding / peptidyl-cysteine oxidation / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / positive regulation of cellular respiration / Mitochondrial protein import / regulation of protein export from nucleus / protein maturation by protein folding / mitochondrial DNA repair / protein-disulfide reductase activity ...'de novo' post-translational protein folding / peptidyl-cysteine oxidation / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / positive regulation of cellular respiration / Mitochondrial protein import / regulation of protein export from nucleus / protein maturation by protein folding / mitochondrial DNA repair / protein-disulfide reductase activity / cellular response to leukemia inhibitory factor / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrion
Similarity search - Function
Helix Hairpins - #2900 / Mitochondrial intermembrane space import and assembly protein 40 / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial intermembrane space import and assembly protein 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsThe pdb submitted file contains the coordinates of the folded region of the protein. Residues 1-44 ...The pdb submitted file contains the coordinates of the folded region of the protein. Residues 1-44 and 110-146 are therefore missing as not well-structured.
AuthorsCiofi Baffoni, S. / Bertini, I. / Gallo, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: MIA40 is an oxidoreductase that catalyzes oxidative protein folding in mitochondria.
Authors: Banci, L. / Bertini, I. / Cefaro, C. / Ciofi-Baffoni, S. / Gallo, A. / Martinelli, M. / Sideris, D.P. / Katrakili, N. / Tokatlidis, K.
History
DepositionMay 8, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...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

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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


Theoretical massNumber of molelcules
Total (without water)16,4041
Polymers16,4041
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 / 400target function
RepresentativeModel #1fewest violations

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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: 16403.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHCHD4, MIA40 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami-pLysS / References: UniProt: Q8N4Q1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The pdb submitted file contains the coordinates of the folded region of the protein. Residues 1-44 and 110-146 are therefore missing as not well-structured.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1323D CBCA(CO)NH
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D HN(CO)CA
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11123D (H)CCH-TOCSY
11212D 1H-1H TOCSY
11323D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 15N] Human Mia40, 2 mM DTT, 50 mM potassium phosphate, 0.5 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] Human Mia40, 2 mM DTT, 50 mM potassium phosphate, 0.5 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHuman Mia40[U-100% 15N]1
2 mMDTT1
50 mMpotassium phosphate1
0.5 mMEDTA1
0.5 mMHuman Mia40[U-100% 13C; U-100% 15N]2
2 mMDTT2
50 mMpotassium phosphate2
0.5 mMEDTA2
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
PECANEghbalniaprediction of secondary structure
WHAT IFVriendstructure validation
ProcheckNMRLaskowski and MacArthurstructure validation
ATNOSCANDID1.2Herrmann, Guntert and Wuthrichnoes assignment
ATNOSCANDID1.2Herrmann, Guntert and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1321 / NOE intraresidue total count: 230 / NOE long range total count: 256 / NOE medium range total count: 398 / NOE sequential total count: 437 / Protein chi angle constraints total count: 221 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 30 / Protein psi angle constraints total count: 30
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 9.233 ° / Maximum upper distance constraint violation: 0.258 Å

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