1YMM Immune System date Jan 21, 2005
title Tcrhla-Dr2bmbp-Peptide Complex
authors M.Hahn, M.J.Nicholson, J.Pyrdol, K.W.Wucherpfennig
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
Synonym: Hla-Dr2b Alpha
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_strain: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacdb3

Molecule: Hla Class II Histocompatibility Antigen, Dr Beta
Chain: B
Synonym: Hla-Dr2b Beta
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_strain: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacdb3

Molecule: Mbp Peptide
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: T Cell Receptor Alpha Chain
Chain: D
Synonym: Tcr Ob.1a12 Alpha
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_strain: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacdb3

Molecule: T-Cell Receptor Beta Chain
Chain: E
Synonym: Tcr Ob.1a12 Beta
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_strain: Sf9
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacdb3
symmetry Space Group: F 2 2 2
R_factor 0.274 R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
137.340 212.620 278.220 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand NAG enzyme
Primary referenceUnconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor., Hahn M, Nicholson MJ, Pyrdol J, Wucherpfennig KW, Nat Immunol 2005 May;6(5):490-6. Epub 2005 Apr 10. PMID:15821740
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (1ymm.pdb1.gz) 119 Kb
  • LPC: Ligand-Protein Contacts for 1YMM
  • CSU: Contacts of Structural Units for 1YMM
  • Likely Quarternary Molecular Structure file(s) for 1YMM
  • Structure Factors (260 Kb)
  • Retrieve 1YMM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YMM from S2C, [Save to disk]
  • Re-refined 1ymm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YMM 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 1YMM
  • 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 1YMM, from MSDmotif at EBI
  • Fold representative 1ymm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ymm_A] [1ymm] [1ymm_C] [1ymm_E] [1ymm_D] [1ymm_B]
  • SWISS-PROT database: [P01911] [P01903] [P02686] [P01848] [P01850]
  • Domain organization of [2B1F_HUMAN] [DRA_HUMAN] [MBP_HUMAN] [TCA_HUMAN] [TCB_HUMAN] by SWISSPFAM
  • Domains found in 1YMM: [IG] [IGc1] [IGv] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1YMM with the sequences similar proteins can be viewed for 1YMM's classification [2B1F_HUMAN] [DRA_HUMAN] [MBP_HUMAN] [TCA_HUMAN] [TCB_HUMAN] 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 [2B1F_HUMAN] [DRA_HUMAN] [MBP_HUMAN] [TCA_HUMAN] [TCB_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YMM
  • Community annotation for 1YMM 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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