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- PDB-2e2z: Solution NMR structure of yeast Tim15, co-chaperone of mitochondr... -

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Basic information

Entry
Database: PDB / ID: 2e2z
TitleSolution NMR structure of yeast Tim15, co-chaperone of mitochondrial Hsp70
ComponentsTim15
KeywordsPROTEIN TRANSPORT / CHAPERONE REGULATOR / protein import / zinc finger
Function / homology
Function and homology information


protein import into mitochondrial matrix / response to unfolded protein / mitochondrion organization / protein folding / protein-folding chaperone binding / mitochondrial inner membrane / protein stabilization / mitochondrial matrix / mitochondrion / zinc ion binding
Similarity search - Function
Zinc finger, DNL-type / Mitochondrial import protein TIM15 / DNL zinc finger / Zinc finger DNL-type profile.
Similarity search - Domain/homology
Mitochondrial protein import protein ZIM17
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMomose, T. / Ohshima, C. / Maeda, M. / Endo, T.
CitationJournal: Embo Rep. / Year: 2007
Title: Structural basis of functional cooperation of Tim15/Zim17 with yeast mitochondrial Hsp70
Authors: Momose, T. / Ohshima, C. / Maeda, M. / Endo, T.
History
DepositionNov 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tim15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3952
Polymers11,3291
Non-polymers651
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Tim15 / Uncharacterized protein YNL310C


Mass: 11329.142 Da / Num. of mol.: 1 / Fragment: Tim15 core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42844
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1223D 15N-separated NOESY
1313D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2mM Tim15 U-15N, 13C; 20mM acetate buffer, 50mM NaCl, 10mM ditiothreitol, 0.03mM zinc acetate, zinc sulfate; 99.9% D2O99.9% D2O
21-2mM Tim15 U-15N; 20mM acetate buffer,50mM NaCl,10mM ditiothreitol, 0.03mM zinc acetate, zinc sulfate; 95% H2O,5% D2O95% H2O/5% D2O
31-2mM Tim15; 20mM acetate buffer, 50mM NaCl, 10mM ditiothreitol, 0.03mM zinc acetate, zinc sulfate; 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 4.5 / Pressure: 1 atm / Temperature: 299 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4structure solution
XwinNMR3.5structure solution
Sparky3.11structure solution
CYANA2.1GUENTERT, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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