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- PDB-7clv: Solution structure of mitochondrial Tim23 channel in complex with... -

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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


Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / mitochondrial respiratory chain complex IV assembly / protein insertion into mitochondrial inner membrane / Mitochondrial protein degradation / respiratory chain complex IV / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / protein import into mitochondrial matrix ...Mitochondrial protein import / TIM23 mitochondrial import inner membrane translocase complex / mitochondrion targeting sequence binding / mitochondrial respiratory chain complex IV assembly / protein insertion into mitochondrial inner membrane / Mitochondrial protein degradation / respiratory chain complex IV / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / protein import into mitochondrial matrix / protein transmembrane transporter activity / proton transmembrane transport / intracellular protein transport / mitochondrial intermembrane space / oxidoreductase activity / mitochondrial inner membrane / 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 / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit Vb superfamily / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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

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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

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Experimental details

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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

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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_condition51 atm313.75 K
250 mMPeptide_standard_condition51 atm313.75 K

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NMR measurement

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

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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

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