1T11 | pdb_00001t11

Trigger Factor

• PDB DOI: https://doi.org/10.2210/pdb1T11/pdb

• Classification: CHAPERONE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-04-14 Released: 2004-09-21 
• Deposition Author(s): Ludlam, A.V., Moore, B.A., Xu, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.290 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.242 (DCC) 

Starting Model: experimental

Literature

The crystal structure of ribosomal chaperone trigger factor from Vibrio cholerae.

Ludlam, A.V., Moore, B.A., Xu, Z.

(2004) Proc Natl Acad Sci U S A 101: 13436-13441

• PubMed: 15353602 
• DOI: https://doi.org/10.1073/pnas.0405868101
• Primary Citation Related Structures: 
  1T11


• PubMed Abstract: 
  

  Trigger factor is a molecular chaperone that is present in all species of eubacteria. It binds to the ribosomal 50S subunit near the translation exit tunnel and is thought to be the first protein to interact with nascent polypeptides emerging from the ribosome. The chaperone has a peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the rate-limiting proline isomerization in the protein-folding process. We have determined the crystal structure of nearly full-length trigger factor from Vibrio cholerae by x-ray crystallography at 2.5-A resolution. The structure is composed of two trigger-factor molecules related by a noncrystallographic two-fold symmetry axis. The monomer has an elongated shape and is folded into three domains: an N-terminal domain I that binds to the ribosome, a central domain II that contains PPIase activity, and a C-terminal domain III. The active site of the PPIase domain is occupied by a loop from domain III, suggesting that the PPIase activity of the protein could be regulated. The dimer interface is formed between domains I and III and contains residues of mixed properties. Further implications about dimerization, ribosome binding, and other functions of trigger factor are discussed.

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Organizational Affiliation: 
• Department of Biological Chemistry, Medical School and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.96 kDa 
• Atom Count: 5,898 
• Modeled Residue Count: 750 
• Deposited Residue Count: 784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trigger factor	A, B	392	Vibrio cholerae	Mutation(s): 0  Gene Names: TIG, VC1923 EC: 5.2.1.8
UniProt
Find proteins for Q9KQS5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQS5  Go to UniProtKB:  Q9KQS5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.290 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.242 (DCC) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.86	α = 90
b = 189.86	β = 90
c = 62.06	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
d*TREK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Ludlam, A.V., Moore, B.A., Xu, Z.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description