5HYP

Structure of human C4b-binding protein alpha cain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M28 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein.

Buffalo, C.Z.Bahn-Suh, A.J.Hirakis, S.P.Biswas, T.Amaro, R.E.Nizet, V.Ghosh, P.

(2016) Nat Microbiol 1: 16155-16155

  • DOI: https://doi.org/10.1038/nmicrobiol.2016.155
  • Primary Citation of Related Structures:  
    5HYP, 5HYT, 5HYU, 5HZP, 5I0Q

  • PubMed Abstract: 

    No vaccine exists against group A Streptococcus (GAS), a leading cause of worldwide morbidity and mortality. A severe hurdle is the hypervariability of its major antigen, the M protein, with >200 different M types known. Neutralizing antibodies typically recognize M protein hypervariable regions (HVRs) and confer narrow protection. In stark contrast, human C4b-binding protein (C4BP), which is recruited to the GAS surface to block phagocytic killing, interacts with a remarkably large number of M protein HVRs (apparently ∼90%). Such broad recognition is rare, and we discovered a unique mechanism for this through the structure determination of four sequence-diverse M proteins in complexes with C4BP. The structures revealed a uniform and tolerant 'reading head' in C4BP, which detected conserved sequence patterns hidden within hypervariability. Our results open up possibilities for rational therapies that target the M-C4BP interaction, and also inform a path towards vaccine design.


  • Organizational Affiliation

    Department of Chemistry &Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
M28 protein104Streptococcus pyogenesMutation(s): 0 
Gene Names: emm28
UniProt
Find proteins for W0T1Y4 (Streptococcus pyogenes)
Explore W0T1Y4 
Go to UniProtKB:  W0T1Y4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0T1Y4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.192α = 90
b = 133.192β = 90
c = 133.192γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM007240
American Heart AssociationUnited States14PRE18320032
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI096837
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI077780

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary