5HYT | pdb_00005hyt

Structure of human C4b-binidng protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M22 protein

• PDB DOI: https://doi.org/10.2210/pdb5HYT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Streptococcus pyogenes, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-01 Released: 2016-07-20 
• Deposition Author(s): Buffalo, C.Z., Bahn-Suh, A.J., Ghosh, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

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

• PubMed: 27595425 
• DOI: https://doi.org/10.1038/nmicrobiol.2016.155
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry &Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, USA.
Skaggs School of Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.12 kDa 
• Atom Count: 4,914 
• Modeled Residue Count: 612 
• Deposited Residue Count: 844 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Precursor to Protein Sir22	A, C, F [auth G], H [auth E]	83	Streptococcus pyogenes	Mutation(s): 0  Gene Names: sir22
UniProt
Find proteins for Q54901 (Streptococcus pyogenes) Explore Q54901  Go to UniProtKB:  Q54901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C4b-binding protein alpha chain	B, D, E [auth F], G [auth H]	128	Homo sapiens	Mutation(s): 0  Gene Names: C4BPA, C4BP
UniProt & NIH Common Fund Data Resources
Find proteins for P04003 (Homo sapiens) Explore P04003  Go to UniProtKB:  P04003
PHAROS:  P04003 GTEx:  ENSG00000123838

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.079	α = 90
b = 80.348	β = 90
c = 152.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Buffalo, C.Z., Bahn-Suh, A.J., Ghosh, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM007240
American Heart Association	United States	14PRE18320032
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI096837
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI077780

Revision History  

• 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: 2024-10-23
  Changes: Structure summary