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- PDB-1zu2: Solution NMR structure of the plant Tom20 mitochondrial import re... -

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Basic information

Entry
Database: PDB / ID: 1zu2
TitleSolution NMR structure of the plant Tom20 mitochondrial import receptor from Arabidopsis thaliana
ComponentsMitochondrial import receptor subunit TOM20-3
KeywordsTRANSPORT PROTEIN / TPR / tetratricopeptide repeat like / TPR-like
Function / homology
Function and homology information


TIM23 mitochondrial import inner membrane translocase complex / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein-transporting ATPase activity / protein targeting to mitochondrion / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrion / cytosol
Similarity search - Function
Plant specific mitochondrial import receptor subunit TOM20 / Plant specific mitochondrial import receptor subunit TOM20 / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM20-3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPerry, A.J. / Hulett, J.M. / Lithgow, T. / Gooley, P.R.
Citation
Journal: Curr.Biol. / Year: 2006
Title: Convergent evolution of receptors for protein import into mitochondria
Authors: Perry, A.J. / Hulett, J.M. / Likic, V.A. / Lithgow, T. / Gooley, P.R.
#1: Journal: To be Published
Title: Letter to the Editor: 1H, 13C and 15N Resonance Assignments of the cytosolic domain of Tom20 from Arabidopsis thaliana
Authors: Perry, A.J. / Hulett, J.M. / Lithgow, T. / Gooley, P.R.
History
DepositionMay 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial import receptor subunit TOM20-3


Theoretical massNumber of molelcules
Total (without water)17,9771
Polymers17,9771
Non-polymers00
Water00
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitochondrial import receptor subunit TOM20-3 / Translocase of outer membrane 20 kDa isoform 3


Mass: 17976.834 Da / Num. of mol.: 1 / Fragment: isoform-3 cytosolic receptor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TOM20-3 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta [BL21(DE3) derived] / References: UniProt: P82874

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA
1433D-13C-separated NOESY (aromatics)
1533D 13C-separated NOESY
NMR detailsText: Structure contains 5 non-native residues at the N-terminus (from fusion system protease site) and 8 non-native residues at the C-terminus from a polyhistidine tag.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Tom20 U-15N,13C, 20mM sodium phosphate buffer, 150mM sodium chloride, 0.02 %(w/v) sodium azide, 1mM dithiothreitol, 1mM EDTA, 3mM phenylmethylsulphonylfluoride, 90 % H2O, 10 % D2O90% H2O/10% D2O
21mM Tom20 U-15N, 20mM sodium phosphate buffer, 150mM sodium chloride, 0.02 %(w/v) sodium azide, 1mM dithiothreitol, 1mM EDTA, 3mM phenylmethylsulphonylfluoride, 90 % H2O, 10 % D2O90% H2O/10% D2O
31mM Tom20 U-15N,13C, 20mM sodium phosphate buffer, 150mM sodium chloride, 0.02 %(w/v) sodium azide, 1mM dithiothreitol, 1mM EDTA, 3mM phenylmethylsulphonylfluoride, 95 % D2O95 % D2O
Sample conditionsIonic strength: 150mM sodium chloride / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.1cVarian Inc.collection
NMRPipe1.1Delaglio, F.processing
Sparky3.111Goddard, T.D & Kneller, D.G.data analysis
CYANA1.0.7Guentert, P.structure solution
CANDID1Guentert, P. & Herrmann, T.data analysis
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The CANDID software was used for initial automatic NOE assignment. Structures are based on 1629 NOE-derived upper distance constraints (47 intra residue), 136 distance restraints from ...Details: The CANDID software was used for initial automatic NOE assignment. Structures are based on 1629 NOE-derived upper distance constraints (47 intra residue), 136 distance restraints from hydrogen bonds, refinement against 129 J(HNHA) coupling constants and 234 PHI/PSI dihedral angle constraints from TALOS.
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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