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 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Structural basis for collagen recognition by the Streptococcus pyogenes M3 protein and its involvement in biofilm

Wojnowska, M., Wajima, T., Yelland, T., Ludewig, H., Hagan, R.M., Watt, G., Hamaia, S.W., Bihan, D., Malcor, J.D., Bonna, A., Bergsten, H., Svensson, M., Oppegaard, O., Skrede, S., Arnell, P., Hyldegaard, O., Farndale, R.W., Norrby-Teglund, A., Schwarz-Linek, U.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.12.17.628954

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 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 

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
• Version 1.2: 2025-01-15
  Changes: Database references, Structure summary