Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 11.46 kDa 
• Atom Count: 873 
• Modelled Residue Count: 97 
• Deposited Residue Count: 98 
• Unique protein chains: 1

4PZ1

Crystal structure of a sHIP (UniProt Id: Q99XU0) mutant from Streptococcus pyogenes

• PDB DOI: 10.2210/pdb4PZ1/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-03-28 Released: 2015-03-11 
• Deposition Author(s): Wisniewska, M., Happonen, L., Frick, I.-M., Bjorck, L., Streicher, W., Malmstrom, J., Wikstrom, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes.

Wisniewska, M., Happonen, L., Kahn, F., Varjosalo, M., Malmstrom, L., Rosenberger, G., Karlsson, C., Cazzamali, G., Pozdnyakova, I., Frick, I.M., Bjorck, L., Streicher, W., Malmstrom, J., Wikstrom, M.

(2014) J Biol Chem 289: 18175-18188

• PubMed: 24825900 
• DOI: 10.1074/jbc.M114.565978
• Primary Citation of Related Structures:  
  4MER, 4PZ1


• PubMed Abstract: 
  

Streptococcus pyogenes is a significant bacterial pathogen in the human population. The importance of virulence factors for the survival and colonization of S. pyogenes is well established, and many of these factors are exposed to the extracellular environment, enabling bacterial interactions with the host. In the present study, we quantitatively analyzed and compared S. pyogenes proteins in the growth medium of a strain that is virulent to mice with a non-virulent strain. Particularly, one of these proteins was present at significantly higher levels in stationary growth medium from the virulent strain. We determined the three-dimensional structure of the protein that showed a unique tetrameric organization composed of four helix-loop-helix motifs. Affinity pull-down mass spectrometry analysis in human plasma demonstrated that the protein interacts with histidine-rich glycoprotein (HRG), and the name sHIP (streptococcal histidine-rich glycoprotein-interacting protein) is therefore proposed. HRG has antibacterial activity, and when challenged by HRG, sHIP was found to rescue S. pyogenes bacteria. This and the finding that patients with invasive S. pyogenes infection respond with antibody production against sHIP suggest a role for the protein in S. pyogenes pathogenesis.

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Organizational Affiliation: 

From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sHIP	A	98	Streptococcus pyogenes serotype M1	Mutation(s): 4  Gene Names: M5005_Spy1730, SPy_2034
UniProt
Find proteins for Q99XU0 (Streptococcus pyogenes serotype M1) Explore Q99XU0  Go to UniProtKB:  Q99XU0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.37	α = 90
b = 33.28	β = 90
c = 89.58	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-28 
• Released Date: 2015-03-11 
Deposition Author(s): Wisniewska, M., Happonen, L., Frick, I.-M., Bjorck, L., Streicher, W., Malmstrom, J., Wikstrom, M.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection