Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1BCD 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.46 kDa 
• Atom Count: 5191 
• Residue Count: 612 
• Unique protein chains: 4

1JWU

Crystal Structure of the Complex of the MHC Class II Molecule HLA-DR1 (HA peptide 306-318) with the superantigen SEC3 Variant 3B2

• DOI: 10.2210/pdb1JWU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-09-05 Released: 2003-07-08 
• Deposition Author(s): Sundberg, E.J., Andersen, P.S., Schlievert, P.M., Karjalainen, K., Mariuzza, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Literature

Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation

Sundberg, E.J., Andersen, P.S., Schlievert, P.M., Karjalainen, K., Mariuzza, R.A.

(2003) Structure 11: 1151-1161

• PubMed: 12962633 
• DOI: 10.1016/s0969-2126(03)00187-4
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Due to a paucity of studies that synthesize structural, energetic, and functional analyses of a series of protein complexes representing distinct stages in an affinity maturation pathway, the biophysical basis for the molecular evolution of protein-protein interactions is poorly understood. Here, we combine crystal structures and binding-free energies of a series of variant superantigen (SAG)-major histocompatibility complex (MHC) class II complexes exhibiting increasingly higher affinity to reveal that this affinity maturation pathway is controlled largely by two biophysical factors: shape complementarity and buried hydrophobic surface. These factors, however, do not contribute equivalently to the affinity maturation of the interface, as the former dominates the early steps of the maturation process while the latter is responsible for improved binding in later steps. Functional assays reveal how affinity maturation of the SAG-MHC interface corresponds to T cell activation by SAGs.

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, W.M. Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	A	182	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903 GTEx  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR-1 beta chain	B	190	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911 GTEx  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HA peptide	C	13	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Enterotoxin type C-3	D	239	Staphylococcus aureus	Mutation(s): 4  Gene Names: entC3
Find proteins for P0A0L5 (Staphylococcus aureus) Go to UniProtKB:  P0A0L5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.753	α = 90
b = 171.753	β = 90
c = 120.489	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-05 
• Released Date: 2003-07-08 
Deposition Author(s): Sundberg, E.J., Andersen, P.S., Schlievert, P.M., Karjalainen, K., Mariuzza, R.A.

Revision History 

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance