[English] 日本語
Yorodumi
- PDB-2l0y: Complex hMia40-hCox17 -

+
Open data


ID or keywords:

Loading...

-
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 / copper chaperone activity / mitochondrial respiratory chain complex assembly / mitochondrial cytochrome c oxidase assembly / positive regulation of cellular respiration / copper ion transport / Mitochondrial protein import / protein import into mitochondrial intermembrane space ...'de novo' post-translational protein folding / positive regulation of cytochrome-c oxidase activity / peptidyl-cysteine oxidation / copper chaperone activity / mitochondrial respiratory chain complex assembly / mitochondrial cytochrome c oxidase assembly / positive regulation of cellular respiration / copper ion transport / Mitochondrial protein import / protein import into mitochondrial intermembrane space / ion binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
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

-
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: 7.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
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

+
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