3QLE

Structural Basis for the Function of Tim50 in the Mitochondrial Presequence Translocase

• PDB DOI: https://doi.org/10.2210/pdb3QLE/pdb

• Classification: CHAPERONE
• Organism(s): Saccharomyces cerevisiae EC1118
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-02 Released: 2011-03-02 
• Deposition Author(s): Qian, X.G., Gebert, M., Hpker, J., Yan, M., Li, J.Z., Wiedemann, N., Laan, M.V.D., Pfanner, N., Sha, B.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Structural basis for the function of tim50 in the mitochondrial presequence translocase.

Qian, X., Gebert, M., Hopker, J., Yan, M., Li, J., Wiedemann, N., van der Laan, M., Pfanner, N., Sha, B.

(2011) J Mol Biol 411: 513-519

• PubMed: 21704637 
• DOI: https://doi.org/10.1016/j.jmb.2011.06.020
• Primary Citation of Related Structures:  
  3QLE


• PubMed Abstract: 
  

  Many mitochondrial proteins are synthesized as preproteins carrying amino-terminal presequences in the cytosol. The preproteins are imported by the translocase of the outer mitochondrial membrane and the presequence translocase of the inner membrane. Tim50 and Tim23 transfer preproteins through the intermembrane space to the inner membrane. We report the crystal structure of the intermembrane space domain of yeast Tim50 to 1.83 Å resolution. A protruding β-hairpin of Tim50 is crucial for interaction with Tim23, providing a molecular basis for the cooperation of Tim50 and Tim23 in preprotein translocation to the protein-conducting channel of the mitochondrial inner membrane.

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Organizational Affiliation: 

Department of Cell Biology, University of Alabama at Birmingham, 1918 University Boulevard, Birmingham, AL 35294-0005, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.27 kDa 
• Atom Count: 1,666 
• Modelled Residue Count: 182 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tim50p	A	204	Saccharomyces cerevisiae EC1118	Mutation(s): 0  Gene Names: EC1118_1P2_2410g
UniProt
Find proteins for C8ZIW7 (Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse)) Explore C8ZIW7  Go to UniProtKB:  C8ZIW7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	E [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.109	α = 90
b = 84.109	β = 90
c = 116.549	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Qian, X.G., Gebert, M., Hpker, J., Yan, M., Li, J.Z., Wiedemann, N., Laan, M.V.D., Pfanner, N., Sha, B.D.

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-17
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description