Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.79 kDa 
• Atom Count: 3137 
• Modelled Residue Count: 353 
• Deposited Residue Count: 454 
• Unique protein chains: 1

1JL5

Novel Molecular Architecture of YopM-a Leucine-rich Effector Protein from Yersinia pestis

• PDB DOI: 10.2210/pdb1JL5/pdb

• Classification: TOXIN
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-07-15 Released: 2001-10-10 
• Deposition Author(s): Evdokimov, A.G., Anderson, D.E., Routzahn, K.M., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit.

Evdokimov, A.G., Anderson, D.E., Routzahn, K.M., Waugh, D.S.

(2001) J Mol Biol 312: 807-821

• PubMed: 11575934 
• DOI: 10.1006/jmbi.2001.4973
• Primary Citation of Related Structures:  
  1G9U, 1JL5


• PubMed Abstract: 
  

Many Gram-negative bacterial pathogens employ a contact-dependent (type III) secretion system to deliver effector proteins into the cytosol of animal or plant cells. Collectively, these effectors enable the bacteria to evade the immune response of the infected organism by modulating host-cell functions. YopM, a member of the leucine-rich repeat protein superfamily, is an effector produced by the bubonic plague bacterium, Yersinia pestis, that is essential for virulence. Here, we report crystal structures of YopM at 2.4 and 2.1 A resolution. Among all leucine-rich repeat family members whose atomic coordinates have been reported, the repeating unit of YopM has the least canonical secondary structure. In both crystals, four YopM monomers form a hollow cylinder with an inner diameter of 35 A. The domain that targets YopM for translocation into eukaryotic cells adopts a well-ordered, alpha-helical conformation that packs tightly against the proximal leucine-rich repeat module. A similar alpha-helical domain can be identified in virulence-associated leucine-rich repeat proteins produced by Salmonella typhimurium and Shigella flexneri, and in the conceptual translation products of several open reading frames in Y. pestis.

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Organizational Affiliation: 

Protein Engineering Section Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
outer protein YopM	A	454	Yersinia pestis	Mutation(s): 0  Gene Names: yopM, yop48, YPCD1.26c, y5054, y0059, YP_pCD60
UniProt
Find proteins for P17778 (Yersinia pestis) Explore P17778  Go to UniProtKB:  P17778

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.43	α = 90
b = 149.43	β = 90
c = 191.18	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-15 
• Released Date: 2001-10-10 
Deposition Author(s): Evdokimov, A.G., Anderson, D.E., Routzahn, K.M., Waugh, D.S.

Revision History  

• Version 1.0: 2001-10-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance