Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 57.66 kDa 
• Atom Count: 3982 
• Residue Count: 485 
• Unique protein chains: 3

1P5U

X-ray structure of the ternary Caf1M:Caf1:Caf1 chaperone:subunit:subunit complex

• DOI: 10.2210/pdb1P5U/pdb

• Classification: CHAPERONE, STRUCTURAL PROTEIN
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-04-28 Released: 2003-06-24 
• Deposition Author(s): Zavialov, A.V., Berglund, J., Pudney, A.F., Fooks, L.J., Ibrahim, T.M., MacIntyre, S., Knight, S.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.216 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Structure and Biogenesis of the Capsular F1 Antigen from Yersinia pestis. Preserved Folding Energy Drives Fiber Formation

Zavialov, A.V., Berglund, J., Pudney, A.F., Fooks, L.J., Ibrahim, T.M., MacIntyre, S., Knight, S.D.

(2003) Cell 113: 587-596

• PubMed: 12787500 
• DOI: 10.1016/s0092-8674(03)00351-9
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Most gram-negative pathogens express fibrous adhesive virulence organelles that mediate targeting to the sites of infection. The F1 capsular antigen from the plague pathogen Yersinia pestis consists of linear fibers of a single subunit (Caf1) and serves as a prototype for nonpilus organelles assembled via the chaperone/usher pathway. Genetic data together with high-resolution X-ray structures corresponding to snapshots of the assembly process reveal the structural basis of fiber formation. Comparison of chaperone bound Caf1 subunit with the subunit in the fiber reveals a novel type of conformational change involving the entire hydrophobic core of the protein. The observed conformational change suggests that the chaperone traps a high-energy folding intermediate of Caf1. A model is proposed in which release of the subunit allows folding to be completed, driving fiber formation.

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Related Citations: 

• Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the F1 antigen Caf1MCaf1 chaperonesubunit pre-assembly complex from Yersinia pestis
  Zavialov, A., Berglund, J., Knight, S.D.
  (2003) Acta Crystallogr D Biol Crystallogr 59: 359

• Donor strand complementation mechanism in the biogenesis of non-pilus systems
  Zavialov, A.V., Kersley, J., Korpela, T., Zav'yalov, V.P., MacIntyre, S., Knight, S.D.
  (2002) Mol Microbiol 45: 983

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Organizational Affiliation: 

Department of Molecular Biosciences/Structural Biology, Uppsala Biomedical Center, Swedish University of Agricultural Sciences, Box 590, SE-751 24 Uppsala, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Chaperone protein Caf1M	A	235	Yersinia pestis	Mutation(s): 0  Gene Names: caf1M, YPMT1.82, Y1098, YP_pMT084
Find proteins for P26926 (Yersinia pestis) Go to UniProtKB:  P26926

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
F1 capsule antigen	B	149	Yersinia pestis	Mutation(s): 1  Gene Names: caf1, YPMT1.84, Y1100, YP_pMT082
Find proteins for P26948 (Yersinia pestis) Go to UniProtKB:  P26948

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
F1 capsule antigen	C	147	Yersinia pestis	Mutation(s): 0  Gene Names: caf1, YPMT1.84, Y1100, YP_pMT082
Find proteins for P26948 (Yersinia pestis) Go to UniProtKB:  P26948

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.216 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.816	α = 90
b = 69.62	β = 90
c = 45.271	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-28 
• Released Date: 2003-06-24 
Deposition Author(s): Zavialov, A.V., Berglund, J., Pudney, A.F., Fooks, L.J., Ibrahim, T.M., MacIntyre, S., Knight, S.D.

Revision History 

• Version 1.0: 2003-06-24
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance