1SEB Complex (Mhc Ii Peptide Toxin) date Nov 26, 1995
title Complex Of The Human Mhc Class II Glycoprotein Hla-Dr1 And The Bacterial Superantigen Seb
authors T.S.Jardetzky, J.H.Brown, J.C.Gorga, L.J.Stern, R.G.Urban, Y.I.Chi, C.Stauffacher, J.L.Strominger, D.C.Wiley
compound source
Molecule: Hla Class II Histocompatibility Antigen
Chain: A, E
Fragment: Extracellular Domain
Synonym: Hla-Dr1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Cell_line: Lg-2
Expression_system: Homo Sapiens
Expression_system_cell_line: Lg-2 Cells

Molecule: Hla Class II Histocompatibility Antigen
Chain: B, F
Fragment: Extracellular Domain
Synonym: Hla-Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Cell_line: Lg-2
Expression_system: Homo Sapiens
Expression_system_cell_line: Lg-2 Cells

Molecule: Endogenous Peptide Model, Poly-Ala
Chain: C, G
Other_details: Superposition Of Many Different Peptides

Organism_scientific: Homo Sapiens
Organism_common: Human

Molecule: Enterotoxin Type B
Chain: D, H
Synonym: Seb

Organism_scientific: Staphylococcus Aureus
Cell_line: Lg-2
symmetry Space Group: P 21 21 21
R_factor 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.000 114.700 149.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
related structures by homologous chain: 1A6A, 1IEB, 1SE2
similarity Belongs to the mhc class ii family. Belongs to the staphylococcal/streptococcal toxin family. Contains 1 ig-like c1-type (immunoglobulin-like) domain.[MHC_II_alpha]
subunit Heterodimer of an alpha chain and a beta chain.
polymorphism The following alleles of drb1-1 are known: drb1*0101, drb1*0102, drb1*0103, drb1*0104, drb1*0105, drb1*0106 and drb1*0107. The sequence shown is that of dra*0101. The following alleles of dra are known dra*0102. The sequence shown is that of drb1*0101.
subcellular loc. Secreted protein. Membrane; single-pass type i membrane protein.
Genes ENTB (S. aureus); HLA-DRA1, HLA-DRA, HLA-DRB1 (H. sapiens)
function The illness characterized by high fever, hypotension, diarrhea, shock, and in some cases death. Staphylococcal enterotoxins cause the intoxication staphylococcal food poisoning syndrome.
Gene
Ontology
ChainFunctionProcessComponent
H
  • pathogenesis
  • extracellular region
  • Primary referenceThree-dimensional structure of a human class II histocompatibility molecule complexed with superantigen., Jardetzky TS, Brown JH, Gorga JC, Stern LJ, Urban RG, Chi YI, Stauffacher C, Strominger JL, Wiley DC, Nature 1994 Apr 21;368(6473):711-8. PMID:8152483
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (196 Kb) [Save to disk]
  • Biological Unit Coordinates (1seb.pdb1.gz) 191 Kb
  • CSU: Contacts of Structural Units for 1SEB
  • Likely Quarternary Molecular Structure file(s) for 1SEB
  • Retrieve 1SEB in mmCIF format [Save to disk]
  • View 1SEB in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
  • Visual 3D analysis of 1SEB
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1SEB, from MSDmotif at EBI
  • Genome occurence of 1SEB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1seba2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1seba1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1sebb2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1sebb1, region B:93-192 [Jmol] [rasmolscript] [script source]
        - Domain d1sebd2, region D:127-235 [Jmol] [rasmolscript] [script source]
        - Domain d1sebd1, region D:2-121 [Jmol] [rasmolscript] [script source]
        - Domain d1sebe2, region E:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1sebe1, region E:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1sebf2, region F:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1sebf1, region F:93-192 [Jmol] [rasmolscript] [script source]
        - Domain d1sebh2, region H:127-235 [Jmol] [rasmolscript] [script source]
        - Domain d1sebh1, region H:2-121 [Jmol] [rasmolscript] [script source]
  • Fold representative 1seb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1seb_A] [1seb_H] [1seb_G] [1seb_F] [1seb_C] [1seb_B] [1seb_D] [1seb_E]
  • Other resources with information on 1SEB
  • InterPro: IPR001003 , IPR007110 , IPR006173 , IPR003006 , IPR006177 , IPR000353 , IPR006126 , IPR006123 , IPR003597
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1SEB from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2007
    Bioinformatics and Biological Computing
    Weizmann Institute of Science