1J8H Immune System date May 21, 2001
title Crystal Structure Of A Complex Of A Human Alphabeta-T Cell Influenza Ha Antigen Peptide, And Mhc Class II Molecule, Hl
authors J.Hennecke, D.C.Wiley
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
Fragment: Extracellular Domain
Synonym: Hla-Dr1, Dra
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_cell_line: Schneider

Molecule: Hla Class II Histocompatibility Antigen, Dr-4 Bet
Chain: B
Fragment: Extracellular Domain
Synonym: Hla-Dr4, Drb10401
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_cell_line: Schneider

Molecule: Hemagglutinin Ha1 Peptide Chain
Chain: C
Fragment: Antigen Peptide
Engineered: Yes

Organism_scientific: Influenzavirus A
Organism_taxid: 197911
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: T-Cell Receptor Alpha Chain
Chain: D
Fragment: Extracellular Domain
Synonym: Tcr Ha1.7 Alpha Chain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: T-Cell Receptor Beta Chain
Chain: E
Fragment: Extracellular Domain
Synonym: Tcr Ha1.7 Beta Chain
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1
symmetry Space Group: C 1 2 1
R_factor 0.211 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
143.753 73.317 123.033 90.00 108.52 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand NAG, NDG enzyme
related structures by homologous chain: 1KGC, 1KLG, 1KTD, 1LP9, 1MI5, 1SBB
Primary referenceStructure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity., Hennecke J, Wiley DC, J Exp Med 2002 Mar 4;195(5):571-81. PMID:11877480
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (1j8h.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 1J8H
  • CSU: Contacts of Structural Units for 1J8H
  • Likely Quarternary Molecular Structure file(s) for 1J8H
  • Structure Factors (519 Kb)
  • Retrieve 1J8H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1J8H from S2C, [Save to disk]
  • Re-refined 1j8h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1J8H 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 1J8H
  • 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 1J8H, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1j8ha2, region A:2-81 [Jmol] [rasmolscript] [script source]
        - Domain d1j8ha1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1j8hb2, region B:3-92 [Jmol] [rasmolscript] [script source]
        - Domain d1j8hb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1j8hd1, region D:1-117 [Jmol] [rasmolscript] [script source]
        - Domain d1j8hd2, region D:118-203 [Jmol] [rasmolscript] [script source]
        - Domain d1j8he2, region E:119-246 [Jmol] [rasmolscript] [script source]
        - Domain d1j8he1, region E:2-118 [Jmol] [rasmolscript] [script source]
  • Fold representative 1j8h 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: [1j8h_C] [1j8h_D] [1j8h_B] [1j8h_E] [1j8h] [1j8h_A]
  • SWISS-PROT database: [P13760] [P01903] [P03437] [P01850] [P01737]
  • Domain organization of [2B14_HUMAN] [DRA_HUMAN] [HEMA_I68A0] [TCB_HUMAN] [TVA3_HUMAN] by SWISSPFAM
  • Domains found in 1J8H: [IG] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1J8H with the sequences similar proteins can be viewed for 1J8H's classification [2B14_HUMAN] [DRA_HUMAN] [HEMA_I68A0] [TCB_HUMAN] [TVA3_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 [2B14_HUMAN] [DRA_HUMAN] [HEMA_I68A0] [TCB_HUMAN] [TVA3_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1J8H
  • Community annotation for 1J8H at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • 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, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science