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- PDB-2mf7: Solution structure of the ims domain of the mitochondrial import ... -

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Basic information

Entry
Database: PDB / ID: 2mf7
TitleSolution structure of the ims domain of the mitochondrial import protein TIM21 from S. cerevisiae
ComponentsMitochondrial import inner membrane translocase subunit TIM21
KeywordsPROTEIN TRANSPORT / membrane / mitochondria / translocation / mitochondrial import protein / IMS domain
Function / homology
Function and homology information


TIM23 mitochondrial import inner membrane translocase complex / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim21 / Mitochondrial import inner membrane translocase subunit Tim21 / Tim21 IMS domain superfamily / TIM21 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit TIM21
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model9
AuthorsBajaj, R. / Jaremko, L. / Jaremko, M. / Becker, S. / Zweckstetter, M.
CitationJournal: Structure / Year: 2014
Title: Molecular Basis of the Dynamic Structure of the TIM23 Complex in the Mitochondrial Intermembrane Space.
Authors: Bajaj, R. / Jaremko, L. / Jaremko, M. / Becker, S. / Zweckstetter, M.
History
DepositionOct 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: 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: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial import inner membrane translocase subunit TIM21


Theoretical massNumber of molelcules
Total (without water)14,7631
Polymers14,7631
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Mitochondrial import inner membrane translocase subunit TIM21


Mass: 14763.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TIM21, YGR033C / Production host: Escherichia coli (E. coli) / References: UniProt: P53220

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.3-0.8 mM [U-100% 13C; U-100% 15N] entity, 50 mM sodium chloride, 20 mM HEPES, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-100% 13C; U-100% 15N]0.3-0.81
50 mMsodium chloride-21
20 mMHEPES-31
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: refinement in explicit solvent
NMR constraintsNOE constraints total: 3100 / NOE intraresidue total count: 947 / NOE long range total count: 1088 / NOE medium range total count: 378 / NOE sequential total count: 687
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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