- PDB-2k3j: The solution structure of human Mia40 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2k3j
Title
The solution structure of human Mia40
Components
Mitochondrial intermembrane space import and assembly protein 40
Keywords
OXIDOREDUCTASE / 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 / positive regulation of cellular respiration / mitochondrial respiratory chain complex assembly / Mitochondrial protein import / regulation of protein export from nucleus / protein import into mitochondrial intermembrane space / protein maturation by protein folding / mitochondrial DNA repair / protein-disulfide reductase activity ...'de novo' post-translational protein folding / peptidyl-cysteine oxidation / positive regulation of cellular respiration / mitochondrial respiratory chain complex assembly / Mitochondrial protein import / regulation of protein export from nucleus / protein import into mitochondrial intermembrane space / 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
The 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.
Mitochondrialintermembranespaceimportandassemblyprotein40 / 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
Experiment
Method: 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-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
1
2D 1H-1H NOESY
1
3
2
3DCBCA(CO)NH
1
4
2
3D HNCO
1
5
2
3D HNCA
1
6
2
3D HN(CA)CB
1
7
2
3DHBHA(CO)NH
1
8
2
3DHN(CO)CA
1
9
1
3D 1H-15N NOESY
1
10
2
3D 1H-13C NOESY
1
11
2
3D (H)CCH-TOCSY
1
12
1
2D 1H-1H TOCSY
1
13
2
3DHN(CA)CO
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.5-1 mM [U-100% 15N] Human Mia40, 2 mM DTT, 50 mM potassium phosphate, 0.5 mM EDTA, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.5-1 mM [U-100% 13C; U-100% 15N] Human Mia40, 2 mM DTT, 50 mM potassium phosphate, 0.5 mM EDTA, 90% H2O/10% D2O
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... andKollm
refinement
Amber
8
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... andKollm
geometryoptimization
CARA
KellerandWuthrich
peakpicking
CARA
KellerandWuthrich
chemicalshiftassignment
PECAN
Eghbalnia
predictionofsecondarystructure
WHAT IF
Vriend
structurevalidation
ProcheckNMR
LaskowskiandMacArthur
structurevalidation
ATNOSCANDID
1.2
Herrmann, GuntertandWuthrich
noesassignment
ATNOSCANDID
1.2
Herrmann, GuntertandWuthrich
peakpicking
Refinement
Method: molecular dynamics / Software ordinal: 1
NMR constraints
NOE 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 representative
Selection criteria: fewest violations
NMR ensemble
Conformer 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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