1JWM Immune System date Sep 04, 2001
title Crystal Structure Of The Complex Of The Mhc Class II Molecule Hla-Dr1(Ha Peptide 306-318) With The Superantigen Sec3
authors E.J.Sundberg, P.S.Andersen, P.M.Schlievert, K.Karjalainen, R.A.Mariuzza
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain;
Chain: A
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Hla Class II Histocompatibility Antigen, Dr-1 Beta Chain;
Chain: B
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ha Peptide
Chain: C
Engineered: Yes
Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized

Molecule: Enterotoxin Type C-3
Chain: D
Synonym: Sec3
Engineered: Yes
Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3
R_factor 0.192 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
171.695 171.695 120.796 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
related structures by homologous chain: 1IEB, 1JWS, 1KG0, 1SE2
Gene
Ontology
ChainFunctionProcessComponent
D
  • pathogenesis
  • extracellular region
    • Primary referenceStructural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation., Sundberg EJ, Andersen PS, Schlievert PM, Karjalainen K, Mariuzza RA, Structure (Camb) 2003 Sep;11(9):1151-61. PMID:12962633
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (1jwm.pdb1.gz) 106 Kb
  • CSU: Contacts of Structural Units for 1JWM
  • Likely Quarternary Molecular Structure file(s) for 1JWM
  • Structure Factors (479 Kb)
  • Retrieve 1JWM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JWM from S2C, [Save to disk]
  • Re-refined 1jwm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1JWM 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 1JWM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1JWM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jwma2, region A:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1jwma1, region A:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1jwmb2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1jwmb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1jwmd1, region D:1-121 [Jmol] [rasmolscript] [script source]
        - Domain d1jwmd2, region D:122-239 [Jmol] [rasmolscript] [script source]
  • Fold representative 1jwm 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: [1jwm_A] [1jwm_B] [1jwm_C] [1jwm_D]
  • SWISS-PROT database: [P04229] [P01903] [P0A0L5]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] by SWISSPFAM
  • Domains found in 1JWM: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1JWM with the sequences similar proteins can be viewed for 1JWM's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1JWM
  • Community annotation for 1JWM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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