Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.77 kDa 
• Atom Count: 193 
• Modelled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique protein chains: 1

1KDL

Solution structure of the amphipathic domain of YopD from Yersinia

• PDB DOI: 10.2210/pdb1KDL/pdb

• Classification: STRUCTURAL PROTEIN
• Mutation(s): No 


• Deposited: 2001-11-13 Released: 2002-08-21 
• Deposition Author(s): Tengel, T., Sethson, I., Francis, M.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 1 
• Selection Criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy 

Literature

Conformational analysis by CD and NMR spectroscopy of a peptide encompassing the amphipathic domain of YopD from Yersinia.

Tengel, T., Sethson, I., Francis, M.S.

(2002) Eur J Biochem 269: 3659-3668

• PubMed: 12153562 
• DOI: 10.1046/j.1432-1033.2002.03051.x
• Primary Citation of Related Structures:  
  1KDL


• PubMed Abstract: 
  

To establish an infection, Yersinia pseudotuberculosis utilizes a plasmid-encoded type III secretion machine that permits the translocation of several anti-host factors into the cytosol of target eukaryotic cells. Secreted YopD is essential for this process. Pre-secretory stabilization of YopD is mediated by an interaction with its cognate chaperone, LcrH. YopD possesses LcrH binding domains located in the N-terminus and in a predicted amphipathic domain located near the C-terminus. This latter domain is also critical for Yersinia virulence. In this study, we designed synthetic peptides encompassing the C-terminal amphipathic domain of YopD. A solution structure of YopD278-300, a peptide that strongly interacted with LcrH, was obtained by NMR methods. The structure is composed of a well-defined amphipathic alpha helix ranging from Phe280 to Tyr291, followed by a type I beta turn between residues Val292 and His295. The C-terminal truncated peptides, YopD278-292 and YopD271-292, lacked helical structure, implicating the beta turn in helix stability. An interaction between YopD278-300 and its cognate chaperone, LcrH, was observed by NMR through line-broadening effects and chemical shift differences between the free peptide and the peptide-LcrH complex. These effects were not observed for the unstructured peptide, YopD278-292, which confirms that the alpha helical structure of the YopD amphipathic domain is a critical binding region of LcrH.

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Organizational Affiliation: 

Department of Organic Chemistry, Umeå University, Umeå, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YOPD protein	A	23	N/A	Mutation(s): 0
UniProt
Find proteins for Q06131 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q06131  Go to UniProtKB:  Q06131

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 1 
• Selection Criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy 
• OLDERADO: 1KDL Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-13 
• Released Date: 2002-08-21 
Deposition Author(s): Tengel, T., Sethson, I., Francis, M.S.

Revision History  

• Version 1.0: 2002-08-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations