1L0Y Immune System date Feb 14, 2002
title T Cell Receptor Beta Chain Complexed With Superantigen Spea With Zinc
authors H.Li, E.J.Sundberg, R.A.Mariuzza
compound source
Molecule: 14.3.D T Cell Receptor Beta Chain
Chain: A, C
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell_line: J558l

Molecule: Exotoxin Type A
Chain: B, D
Synonym: Scarlet Fever Toxin, Erythrogenic Toxin, Spe A
Engineered: Yes
Mutation: Yes

Organism_scientific: Streptococcus Pyogenes
Organism_taxid: 1314
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.221 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.722 83.734 93.900 90.00 91.74 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand GOL, ZN enzyme
related structures by homologous chain: 1B1Z, 1FNU, 1TCR
Gene
Ontology
ChainFunctionProcessComponent
D, B


Primary referenceStructures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes., Sundberg EJ, Li H, Llera AS, McCormick JK, Tormo J, Schlievert PM, Karjalainen K, Mariuzza RA, Structure (Camb) 2002 May;10(5):687-99. PMID:12015151
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (157 Kb) [Save to disk]
  • Biological Unit Coordinates (1l0y.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (1l0y.pdb2.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 1L0Y
  • CSU: Contacts of Structural Units for 1L0Y
  • Likely Quarternary Molecular Structure file(s) for 1L0Y
  • Structure Factors (273 Kb)
  • Retrieve 1L0Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1L0Y from S2C, [Save to disk]
  • Re-refined 1l0y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1L0Y 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.
  • Visual 3D analysis of 1L0Y
  • 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 1L0Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l0ya2, region A:118-244 [Jmol] [rasmolscript] [script source]
        - Domain d1l0ya1, region A:3-117 [Jmol] [rasmolscript] [script source]
        - Domain d1l0yb1, region B:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1l0yb2, region B:108-220 [Jmol] [rasmolscript] [script source]
        - Domain d1l0yc2, region C:118-244 [Jmol] [rasmolscript] [script source]
        - Domain d1l0yc1, region C:3-117 [Jmol] [rasmolscript] [script source]
        - Domain d1l0yd1, region D:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1l0yd2, region D:108-221 [Jmol] [rasmolscript] [script source]
  • Fold representative 1l0y 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: [1l0y_C] [1l0y_D] [1l0y] [1l0y_A] [1l0y_B]
  • SWISS-PROT database: [P62561] [P62560] [P01851]
  • Domain organization of [SPEA_STRP8] [SPEA_STRPY] [TCB2_MOUSE] by SWISSPFAM
  • Domains found in 1L0Y: [IG_like] [IGv ] by SMART
  • Other resources with information on 1L0Y
  • Community annotation for 1L0Y at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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