8P6J

Structure of the hypervariable region of Streptococcus pyogenes M3 protein in complex with a collagen peptide

• PDB DOI: https://doi.org/10.2210/pdb8P6J/pdb

• Classification: PROTEIN BINDING
• Organism(s): Streptococcus pyogenes serotype M3, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-26 Released: 2023-06-21 
• Deposition Author(s): Wojnowska, M., Schwarz-Linek, U.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.285 
• R-Value Work: 0.241 

Literature

Structural basis for collagen recognition by the Streptococcus pyogenes M3 protein

Wojnowska, M., Yelland, T., Ludewig, H., Hagan, R.M., Watt, G., Hamaia, S., Bihan, D., Farndale, R.W., Schwarz-Linek, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66 kDa 
• Atom Count: 4,046 
• Modelled Residue Count: 562 
• Deposited Residue Count: 596 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiphagocytic M protein, type 3	A [auth BBB], B [auth CCC], F [auth FFF], G [auth GGG]	113	Streptococcus pyogenes serotype M3	Mutation(s): 0  Gene Names: emm3, SpyM3_1727
UniProt
Find proteins for A0A0H2UWN1 (Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)) Explore A0A0H2UWN1  Go to UniProtKB:  A0A0H2UWN1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
collagen II-27 Toolkit peptide (JDM238)	C [auth AAA], D [auth DDD], E [auth EEE], H [auth HHH], I [auth JJJ], J [auth III]	24	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	C [auth AAA], D [auth DDD], E [auth EEE], H [auth HHH], I [auth JJJ], J [auth III]	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.285 
• R-Value Work: 0.241 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.832	α = 87.326
b = 51.503	β = 84.78
c = 80.186	γ = 89.394

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Wojnowska, M., Schwarz-Linek, U.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009681/1

Revision History  

• Version 1.0: 2023-06-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary