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- PDB-6k8q: Solution structure of the intermembrane space domain of the mitoc... -

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Basic information

Entry
Database: PDB / ID: 6k8q
TitleSolution structure of the intermembrane space domain of the mitochondrial import protein Tim21 from S. cerevisiae
ComponentsMitochondrial import inner membrane translocase subunit TIM21
KeywordsPROTEIN TRANSPORT / membrane / mitochondria / translocation
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
AuthorsBala, S. / Shinya, S. / Srivastava, A. / Shimada, A. / Kobayashi, N. / Kojima, C. / Tama, F. / Miyashita, O. / Kohda, D.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP26119002 Japan
Japan Society for the Promotion of ScienceJP19H05452 Japan
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.
Authors: Bala, S. / Shinya, S. / Srivastava, A. / Ishikawa, M. / Shimada, A. / Kobayashi, N. / Kojima, C. / Tama, F. / Miyashita, O. / Kohda, D.
History
DepositionJun 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
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

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Assembly

Deposited unit
A: Mitochondrial import inner membrane translocase subunit TIM21


Theoretical massNumber of molelcules
Total (without water)13,5721
Polymers13,5721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8600 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitochondrial import inner membrane translocase subunit TIM21


Mass: 13571.599 Da / Num. of mol.: 1 / Fragment: intermembrane space domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIM21, YGR033C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P53220

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CB
191isotropic13D CBCA(CO)NH
181isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
161isotropic23D 1H-13C NOESY aliphatic
1111isotropic23D 1H-13C NOESY aromatic
1101isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
323 uMTim21[U-13C; U-15N]1
20 mMTRISnatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MagRO-NMRViewNaohiro Kobayashi, Osaka Universitypeak picking
MagRO-NMRViewNaohiro Kobayashi, Osaka Universitychemical shift assignment
MagRO-NMRViewNaohiro Kobayashi, Osaka Universitydata analysis
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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