1P5U Chaperone, Structural Protein date Apr 28, 2003
title X-Ray Structure Of The Ternary Caf1m:Caf1:Caf1 Chaperone:Subunit:Subunit Complex
authors A.V.Zavialov, J.Berglund, A.F.Pudney, L.J.Fooks, T.M.Ibrahim, S.Macintyre, S.D.Knight
compound source
Molecule: Chaperone Protein Caf1m
Chain: A
Fragment: Residues 24-258 Of Sws P26926
Synonym: Caf1m Chaperone; Caf1m; Capsule Protein Fraction 1; F1 Chaperone Protein;
Engineered: Yes
Organism_scientific: Yersinia Pestis
Organism_common: Bacteria
Strain: Kim5
Gene: Caf1m
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_variant: B834 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfm-1-6h

Molecule: F1 Capsule Antigen
Chain: B
Fragment: Residues 22-170 Of Sws P26948
Engineered: Yes
Mutation: Yes
Other_details: Larger Fragment Of F1 Capsule With A9r Mutation;

Organism_scientific: Yersinia Pestis
Organism_common: Bacteria
Strain: Kim5
Gene: Caf1
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_variant: B834 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfm-1-6h

Molecule: F1 Capsule Antigen
Chain: C
Fragment: Residues 35-170 Of Sws P26948
Engineered: Yes
Other_details: Smaller His-Tagged Fragment Of F1 Capsule

Organism_scientific: Yersinia Pestis
Organism_common: Bacteria
Strain: Kim5
Gene: Caf1
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_variant: B834 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfm-1-6h
symmetry Space Group: P 21 21 2
R_factor 0.166
crystal
cell
length a length b length c angle alpha angle beta angle gamma
178.816 69.620 45.271 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.99 Å
similarity Belongs to the periplasmic pilus chaperone family. Contains 1 ig-like (immunoglobulin-like) domain.[Pili_assembly_N]
subcellular loc. Periplasmic. Capsule.
genes caf1, caf1M, pMT082, pMT084, y1098, y1100, y5194, y5196 (Y. pestis)
function It seems to interact with the subunit polypeptide and to prevent it from digestion by a protease. Has a stimulatory role for the envelope antigen f1 secretion.
Gene
Ontology
ChainFunctionProcessComponent
A
  • protein binding
  • unfolded protein binding
  • protein folding
  • cell wall organization and b...
  • outer membrane-bounded perip...
  • periplasmic space
  • C, B


    Primary referenceStructure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation., Zavialov AV, Berglund J, Pudney AF, Fooks LJ, Ibrahim TM, MacIntyre S, Knight SD, Cell 2003 May 30;113(5):587-96. PMID:12787500
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (1p5u.pdb1.gz) 81 Kb
  • CSU: Contacts of Structural Units for 1P5U
  • Likely Quarternary Molecular Structure file(s) for 1P5U
  • Retrieve 1P5U in mmCIF format [Save to disk]
  • View 1P5U in 3D
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • On AstexViewer, from MSD-EBI (viewer documentation).
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  • Cartoon representation from PDB Cartoon
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  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1P5U, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1p5ua2, region A:148-234 [Jmol] [rasmolscript] [script source]
        - Domain d1p5ua1, region A:9-147 [Jmol] [rasmolscript] [script source]
        - Domain d1p5ub_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1p5uc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1p5u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1p5u_C] [1p5u_A] [1p5u_B]
  • Other resources with information on 1P5U
  • InterPro: IPR001829
  • MMDB (Entrez's Structure Database)
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