3TVY

Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions.

Krishnan, V.Dwivedi, P.Kim, B.J.Samal, A.Macon, K.Ma, X.Mishra, A.Doran, K.S.Ton-That, H.Narayana, S.V.

(2013) Acta Crystallogr.,Sect.D 69: 1073-1089

  • DOI: 10.1107/S0907444913004642
  • Primary Citation of Related Structures:  3TW0, 3TXA

  • PubMed Abstract: 
  • The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built an ...

    The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built and a model of full-length GBS104 was generated by combining the homology model (the N1 and N4 domains) and the crystal structure of the 75 kDa fragment (the N2 and N3 domains). This rod-shaped GBS104 model is constructed of three IgG-like domains (the N1, N2 and N4 domains) and one vWFA-like domain (the N3 domain). The N1 and N2 domains of GBS104 are assembled with distinct and remote segments contributed by the N- and C-termini. The metal-binding site in the N3 domain of GBS104 is in the closed/low-affinity conformation. Interestingly, this domain hosts two long arms that project away from the metal-binding site. Using site-directed mutagenesis, two cysteine residues that lock the N3 domain of GBS104 into the open/high-affinity conformation were introduced. Both wild-type and disulfide-locked recombinant proteins were tested for binding to extracellular matrix proteins such as collagen, fibronectin, fibrinogen and laminin, and an increase in fibronectin binding affinity was identified for the disulfide-locked N3 domain, suggesting that induced conformational changes may play a possible role in receptor binding.


    Organizational Affiliation

    UNESCO Regional Centre for Biotechnology (RCB), Gurgaon 122 016, Haryana, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell wall surface anchor family protein
A
373Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)N/A
Find proteins for Q8E0S5 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R))
Go to UniProtKB:  Q8E0S5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.749α = 90.00
b = 101.290β = 90.00
c = 52.665γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
REFMACrefinement
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-05-29
    Type: Database references
  • Version 1.2: 2013-06-19
    Type: Database references