[English] 日本語
Yorodumi
- PDB-7clv: Solution structure of mitochondrial Tim23 channel in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7clv
TitleSolution structure of mitochondrial Tim23 channel in complex with a signaling peptide
Components
  • COX4 isoform 1
  • TIM23 isoform 1
KeywordsPROTEIN TRANSPORT / Membrane Protein / Tim23 Channel / Presequence.
Function / homology
Function and homology information


: / mitochondrion targeting sequence binding / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial cytochrome c oxidase assembly / protein import into mitochondrial matrix / Mitochondrial protein degradation / mitochondrial respiratory chain complex IV / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / protein transmembrane transporter activity ...: / mitochondrion targeting sequence binding / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial cytochrome c oxidase assembly / protein import into mitochondrial matrix / Mitochondrial protein degradation / mitochondrial respiratory chain complex IV / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / protein transmembrane transporter activity / proton transmembrane transport / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity / mitochondrion / zinc ion binding / metal ion binding
Similarity search - Function
: / Mitochondrial inner membrane translocase complex, subunit Tim23 / Tim23-like / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Tim17/Tim22/Tim23/Pmp24 family
Similarity search - Domain/homology
BJ4_G0018620.mRNA.1.CDS.1 / Mitochondrial import inner membrane translocase subunit TIM23 / Cytochrome c oxidase subunit 4, mitochondrial / Mitochondrial import inner membrane translocase subunit TIM23
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsZhou, S. / Ruan, M.S. / Li, Y.Y. / Yang, J. / Richter, C. / Schwalbe, H. / Shen, B. / Wang, J.F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Cell Res. / Year: 2021
Title: Solution structure of the voltage-gated Tim23 channel in complex with a mitochondrial presequence peptide.
Authors: Zhou, S. / Ruan, M. / Li, Y. / Yang, J. / Bai, S. / Richter, C. / Schwalbe, H. / Xie, C. / Shen, B. / Wang, J.
History
DepositionJul 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TIM23 isoform 1
B: TIM23 isoform 1
C: COX4 isoform 1


Theoretical massNumber of molelcules
Total (without water)49,5273
Polymers49,5273
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5760 Å2
ΔGint-34 kcal/mol
Surface area41220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein TIM23 isoform 1


Mass: 23266.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIM23, GI526_G0005095 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5Q5E3, UniProt: P32897*PLUS
#2: Protein/peptide COX4 isoform 1


Mass: 2993.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: COX4, GI526_G0002212 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5PV33, UniProt: P04037*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D TROSY 1H-15N HSQC
122isotropic23D TROSY HNCO
132isotropic23D TROSY HNCA
142isotropic23D TROSY HN(CA)CO
152isotropic23D TROSY CBCA(CO)NH
1102isotropic23D TROSY HN(CA)CB
1203isotropic13D (H)CCH-TOCSY
1193isotropic13D CC(CO)NH
1183isotropic13D H(CCO)NH
193isotropic13D 1H-15N TROSY - NOESY
183isotropic13D 1H-13C TROSY - NOESY
174isotropic13D 1H-15N TROSY - NOESY
164isotropic13D 1H-13C TROSY - NOESY
1115isotropic13D 1H-13C TROSY - NOESY
1136isotropic13D F1-13C/15N-filtered, F3-15N-edited-NOESY-HSQC
1126isotropic13D F1-13C/15N-filtered, F3-13C-edited-NOESY-HSQC
2177isotropic33D HNCO
2167isotropic33D HN(CA)CO
2157isotropic33D CBCA(CO)NH
2147isotropic33D HN(CA)CB
2217isotropic32D 1H-15N HSQC
2227isotropic33D 1H-15N NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.5 mM 2H, 15N Tim23, 90% H2O/10% D2O[2H, 15N]_Tim2390% H2O/10% D2O
micelle20.5 uM 2H, 15N, 13C Tim23_unlabeled_Peptide, 90% H2O/10% D2O[2H, 15N, 13C]_Tim23_unlabeled_Peptide90% H2O/10% D2O
micelle30.5 mM 15N, 13C Tim23_unlabeled_Peptide, 90% H2O/10% D2O[15N, 13C]_Tim23_unlabeled_Peptide90% H2O/10% D2O
micelle40.5 mM 50% 2H, 13C, 15N Tim23_unlabeled_Peptide, 90% H2O/10% D2O[50% 2H, 15N, 13C]_Tim23_unlabeled_Peptide90% H2O/10% D2O
micelle50.5 mM IVL-selectively_labeled_Tim23_unlabeled_peptide Tim23_unlabeled_Peptide, 90% H2O/10% D2OIVL_Selectively_Tim23_unlabeled_Peptide90% H2O/10% D2O
micelle60.5 mM 50%unlabeled/50%labeled_Tim23_unlabeled_peptide Tim23_unlabeled_Peptide, 90% H2O/10% D2O50%unlabeled/50%labeled_Tim23_unlabeled_Peptide90% H2O/10% D2O
micelle70.5 nM 50%unlabeled/50%labeled_Tim23_unlabeled_peptide [15N, 13C]-peptide_unlabeled_Tim23, 90% H2O/10% D2O[15N, 13C]-peptide_unlabeled_Tim2390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTim232H, 15N1
0.5 uMTim23_unlabeled_Peptide2H, 15N, 13C2
0.5 mMTim23_unlabeled_Peptide15N, 13C3
0.5 mMTim23_unlabeled_Peptide50% 2H, 13C, 15N4
0.5 mMTim23_unlabeled_PeptideIVL-selectively_labeled_Tim23_unlabeled_peptide5
0.5 mMTim23_unlabeled_Peptide50%unlabeled/50%labeled_Tim23_unlabeled_peptide6
0.5 nM[15N, 13C]-peptide_unlabeled_Tim2350%unlabeled/50%labeled_Tim23_unlabeled_peptide7
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMTim23_standard_condition5.0 1 atm313.75 K
250 mMPeptide_standard_condition5.0 1 atm313.75 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE9502
Bruker AVANCEBrukerAVANCE8503

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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