8TGT | pdb_00008tgt

Structure of human C4b-binding protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M68 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.344 (Depositor), 0.344 (DCC) 
  • R-Value Work: 
    0.313 (Depositor), 0.312 (DCC) 
  • R-Value Observed: 
    0.316 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TGT

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Conservation of C4BP-binding sequence patterns in Streptococcus pyogenes M and Enn proteins.

Kolesinski, P.McGowan, M.Botteaux, A.Smeesters, P.R.Ghosh, P.

(2024) J Biological Chem 300: 107478-107478

  • DOI: https://doi.org/10.1016/j.jbc.2024.107478
  • Primary Citation Related Structures: 
    8TCB, 8TGT

  • PubMed Abstract: 

    Antigenically sequence variable M proteins of the major bacterial pathogen Streptococcus pyogenes (Strep A) are responsible for recruiting human C4b-binding protein (C4BP) to the bacterial surface, which enables Strep A to evade destruction by the immune system. The most sequence divergent portion of M proteins, the hypervariable region (HVR), is responsible for binding C4BP. Structural evidence points to the conservation of two C4BP-binding sequence patterns (M2 and M22) in the HVR of numerous M proteins, with this conservation applicable to vaccine immunogen design. These two patterns, however, only partially explain C4BP binding by Strep A. Here, we identified several M proteins that lack these patterns but still bind C4BP and determined the structures of two, M68 and M87 HVRs, in complex with a C4BP fragment. Mutagenesis of these M proteins led to the identification of amino acids that are crucial for C4BP binding, enabling formulation of new C4BP-binding patterns. Mutagenesis was also carried out on M2 and M22 proteins to refine or generate experimentally grounded C4BP-binding patterns. The M22 pattern was the most prevalent among M proteins, followed by the M87 and M2 patterns, while the M68 pattern was rare. These patterns, except for M68, were also evident in numerous M-like Enn proteins. Binding of C4BP via these patterns to Enn proteins was verified. We conclude that C4BP-binding patterns occur frequently in Strep A strains of differing M types, being present in their M or Enn proteins, or frequently both, providing further impetus for their use as vaccine immunogens.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, California, USA.

Macromolecule Content 

  • Total Structure Weight: 39.95 kDa 
  • Atom Count: 1,632 
  • Modeled Residue Count: 236 
  • Deposited Residue Count: 336 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M protein
A, B
104Streptococcus pyogenesMutation(s): 0 
Gene Names: emm
UniProt
Find proteins for A0A059T9V1 (Streptococcus pyogenes)
Explore A0A059T9V1 
Go to UniProtKB:  A0A059T9V1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059T9V1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
C4b-binding protein alpha chain128Homo sapiensMutation(s): 0 
Gene Names: C4BPAC4BP
UniProt & NIH Common Fund Data Resources
Find proteins for P04003 (Homo sapiens)
Explore P04003 
Go to UniProtKB:  P04003
PHAROS:  P04003
GTEx:  ENSG00000123838 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04003
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.344 (Depositor), 0.344 (DCC) 
  • R-Value Work:  0.313 (Depositor), 0.312 (DCC) 
  • R-Value Observed: 0.316 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.037α = 90
b = 49.664β = 90
c = 80.403γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesNIH R01 AI154149

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Database references, Structure summary