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- PDB-2bsk: Crystal structure of the TIM9 Tim10 hexameric complex -

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Basic information

Entry
Database: PDB / ID: 2bsk
TitleCrystal structure of the TIM9 Tim10 hexameric complex
Components
  • MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10
  • MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM9 A
KeywordsPROTEIN TRANSPORT / TIM9 / TIM10 / MITOCHONDRIAL PROTEIN IMPORT / TIM COMPLEX
Function / homology
Function and homology information


mitochondrial intermembrane space chaperone complex / TIM22 mitochondrial import inner membrane insertion complex / membrane insertase activity / TIM23 mitochondrial import inner membrane translocase complex / protein insertion into mitochondrial inner membrane / Mitochondrial protein import / protein targeting to mitochondrion / Mitochondrial protein degradation / sensory perception of sound / mitochondrial intermembrane space ...mitochondrial intermembrane space chaperone complex / TIM22 mitochondrial import inner membrane insertion complex / membrane insertase activity / TIM23 mitochondrial import inner membrane translocase complex / protein insertion into mitochondrial inner membrane / Mitochondrial protein import / protein targeting to mitochondrion / Mitochondrial protein degradation / sensory perception of sound / mitochondrial intermembrane space / protein-folding chaperone binding / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / zinc ion binding
Similarity search - Function
Mitochondrial import inner membrane translocase subunit tim13 like domains / : / Tim10-like / Tim10-like domain superfamily / Tim10/DDP family zinc finger / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial import inner membrane translocase subunit Tim10 / Mitochondrial import inner membrane translocase subunit Tim9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsWebb, C.T. / Gorman, M.A. / Lazarus, M. / Ryan, M.T. / Gulbis, J.M.
CitationJournal: Mol.Cell / Year: 2006
Title: Crystal Structure of the Mitochondrial Chaperone Tim910 Reveals a Six-Bladed Alpha-Propeller.
Authors: Webb, C.T. / Gorman, M.A. / Lazarou, M. / Ryan, M.T. / Gulbis, J.M.
History
DepositionMay 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM9 A
B: MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10
C: MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM9 A
D: MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10
E: MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM9 A
F: MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10


Theoretical massNumber of molelcules
Total (without water)63,3486
Polymers63,3486
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.430, 107.430, 110.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM9 A


Mass: 10391.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX 4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI DE3 PLYSS / References: UniProt: Q9Y5J7
#2: Protein MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10


Mass: 10724.161 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX 4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI DE3 PLYSS / References: UniProt: P62072
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growDetails: 0.1 M TRIS-HCL PH 8.5, 28% W/V PEG 3000, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97958
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 3.45→20 Å / Num. obs: 9357 / % possible obs: 89.9 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 3.45→3.6 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.42 / % possible all: 85

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→16 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SIDE CHAINS FOR THE FOLLOWING RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY AND HAVE BEEN MODELLED AS ALANINE RESIDUES. CHAIN A Q13, K15, E16, K58, Q73, L78, L84, L85 CHAIN B E14, K45, ...Details: SIDE CHAINS FOR THE FOLLOWING RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY AND HAVE BEEN MODELLED AS ALANINE RESIDUES. CHAIN A Q13, K15, E16, K58, Q73, L78, L84, L85 CHAIN B E14, K45, K57, D76 CHAIN C D9, Q10, K12, Q13, E16, R39, E44, Q54, K58, Q73 CHAIN D Q7, K57, D60, E63, R64, K67, K68, E77, K81, R82, Q84 CHAIN E Q13, E44, Q54, K58, Q73, Q74, N75 CHAIN F E12, L13, E14, R31, K45, K68, S73
RfactorNum. reflection% reflectionSelection details
Rfree0.3193 481 4.8 %RANDOM
Rwork0.2679 ---
obs0.2679 9357 92.6 %-
Solvent computationBsol: 15.9575 Å2 / ksol: 0.197737 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.953 Å20 Å20 Å2
2---3.953 Å20 Å2
3---7.906 Å2
Refinement stepCycle: LAST / Resolution: 3.3→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 0 3334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008254
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4398
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.3→16 Å
RfactorNum. reflection% reflection
Rfree0.3193 481 4.8 %
Rwork0.2679 8876 -
obs--92.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM

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