PDBsum entry 1jws

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protein Protein-protein interface(s) links
Immune system PDB id
Protein chains
180 a.a. *
187 a.a. *
13 a.a. *
232 a.a. *
Waters ×141
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of the complex of the mhc class ii molecule hla-dr1 (ha peptide 306-318) with the superantigen sec3 variant 3b1
Structure: Hla class ii histocompatibility antigen, dr alpha chain. Chain: a. Engineered: yes. Hla class ii histocompatibility antigen, dr-1 beta chain. Chain: b. Engineered: yes. Ha peptide.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. Staphylococcus aureus. Organism_taxid: 1280.
Biol. unit: Tetramer (from PQS)
2.60Å     R-factor:   0.195     R-free:   0.232
Authors: E.J.Sundberg,P.S.Andersen,P.M.Schlievert,K.Karjalainen, R.A.Mariuzza
Key ref:
E.J.Sundberg et al. (2003). Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation. Structure, 11, 1151-1161. PubMed id: 12962633 DOI: 10.1016/S0969-2126(03)00187-4
05-Sep-01     Release date:   08-Jul-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P01903  (DRA_HUMAN) -  HLA class II histocompatibility antigen, DR alpha chain
254 a.a.
180 a.a.
Protein chain
Pfam   ArchSchema ?
P04229  (2B11_HUMAN) -  HLA class II histocompatibility antigen, DRB1-1 beta chain
266 a.a.
187 a.a.
Protein chain
No UniProt id for this chain
Struc: 13 a.a.
Protein chain
Pfam   ArchSchema ?
P0A0L5  (ENTC3_STAAU) -  Enterotoxin type C-3
266 a.a.
232 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     immune response   3 terms 


DOI no: 10.1016/S0969-2126(03)00187-4 Structure 11:1151-1161 (2003)
PubMed id: 12962633  
Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation.
E.J.Sundberg, P.S.Andersen, P.M.Schlievert, K.Karjalainen, R.A.Mariuzza.
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.
  Selected figure(s)  
Figure 1.
Figure 1. Structural Validation of the Wild-Type and Mutant SEC3-DR1 ComplexesStereodiagrams of composite annealed omit electron density maps in the variant region (residues 43-47) of (A) SEC3-wt, (B) SEC3-3B1, and (C) SEC3-3B2. All electron density maps are contoured at 1.4s. Figure produced using Bobscript (Esnouf, 1997) and Raster3D (Merritt and Bacon, 1997).
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1151-1161) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18545669 C.A.Painter, A.Cruz, G.E.López, L.J.Stern, and Z.Zavala-Ruiz (2008).
Model for the peptide-free conformation of class II MHC proteins.
  PLoS ONE, 3, e2403.  
16829512 M.M.Fernández, R.Guan, C.P.Swaminathan, E.L.Malchiodi, and R.A.Mariuzza (2006).
Crystal structure of staphylococcal enterotoxin I (SEI) in complex with a human major histocompatibility complex class II molecule.
  J Biol Chem, 281, 25356-25364.
PDB code: 2g9h
16260763 H.Li, S.Van Vranken, Y.Zhao, Z.Li, Y.Guo, L.Eisele, and Y.Li (2005).
Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis.
  Protein Sci, 14, 3025-3038.
PDB codes: 2axh 2axj
15537658 M.Hülsmeyer, P.Chames, R.C.Hillig, R.L.Stanfield, G.Held, P.G.Coulie, C.Alings, G.Wille, W.Saenger, B.Uchanska-Ziegler, H.R.Hoogenboom, and A.Ziegler (2005).
A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3.
  J Biol Chem, 280, 2972-2980.
PDB code: 1w72
16338406 S.Cho, C.P.Swaminathan, J.Yang, M.C.Kerzic, R.Guan, M.C.Kieke, D.M.Kranz, R.A.Mariuzza, and E.J.Sundberg (2005).
Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.
  Structure, 13, 1775-1787.  
15698573 Y.Li, Y.Huang, C.P.Swaminathan, S.J.Smith-Gill, and R.A.Mariuzza (2005).
Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces.
  Structure, 13, 297-307.
PDB codes: 1xgp 1xgq 1xgr 1xgt 1xgu
14514664 J.Yang, C.P.Swaminathan, Y.Huang, R.Guan, S.Cho, M.C.Kieke, D.M.Kranz, R.A.Mariuzza, and E.J.Sundberg (2003).
Dissecting cooperative and additive binding energetics in the affinity maturation pathway of a protein-protein interface.
  J Biol Chem, 278, 50412-50421.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.