3DXA Immune System date Jul 23, 2008
title Crystal Structure Of The Dm1 Tcr In Complex With Hla-B4405 Decamer Ebv Antigen
authors J.K.Archbold, W.A.Macdonald, S.Gras, J.Rossjohn
compound source
Molecule: Hla Class I Histocompatibility Complex Hla-B4402
Chain: A, F, K
Synonym: Hla Class I Histocompatibility Antigen, B-44 Alpha Mhc Class I Antigen B44; Bw-44;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-B, Hlab
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26

Molecule: Beta-2-Microglobulin
Chain: B, G, L
Synonym: Beta-2-Microglobulin Form Pi 5.3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26

Molecule: Ebv Decapeptide Epitope
Chain: C, H, M
Fragment: Residues 281-290
Engineered: Yes

Synthetic: Yes
Other_details: Sequence Occurs In Human Herpesvirus 4, Gene Berf3-Berf4;

Molecule: Dm1 T Cell Receptor Alpha Chain
Chain: D, I, N
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26

Molecule: Dm1 T Cell Receptor Beta Chain
Chain: E, J, O
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26
symmetry Space Group: P 65 2 2
R_factor 0.286 R_Free 0.330
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.954 121.954 695.914 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.50 Å
Gene
Ontology
ChainFunctionProcessComponent
G, L, B
  • cellular response to iron io...

  • Primary referenceNatural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition., Archbold JK, Macdonald WA, Gras S, Ely LK, Miles JJ, Bell MJ, Brennan RM, Beddoe T, Wilce MC, Clements CS, Purcell AW, McCluskey J, Burrows SR, Rossjohn J, J Exp Med. 2009 Jan 16;206(1):209-19. Epub 2009 Jan 12. PMID:19139173
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (393 Kb) [Save to disk]
  • Biological Unit Coordinates (3dxa.pdb1.gz) 134 Kb
  • Biological Unit Coordinates (3dxa.pdb2.gz) 133 Kb
  • Biological Unit Coordinates (3dxa.pdb3.gz) 134 Kb
  • CSU: Contacts of Structural Units for 3DXA
  • Likely Quarternary Molecular Structure file(s) for 3DXA
  • Structure Factors (646 Kb)
  • Retrieve 3DXA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DXA from S2C, [Save to disk]
  • Re-refined 3dxa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DXA 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 3DXA
  • 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 3DXA, from MSDmotif at EBI
  • Fold representative 3dxa from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dxa_L] [3dxa_B] [3dxa_F] [3dxa_E] [3dxa_I] [3dxa_A] [3dxa_K] [3dxa_J] [3dxa_O] [3dxa_G] [3dxa_H] [3dxa_D] [3dxa] [3dxa_M] [3dxa_C] [3dxa_N]
  • SWISS-PROT database: [P30481] [P61769] [P03204] [P01848] [P01850]
  • Domain organization of [1B44_HUMAN] [B2MG_HUMAN] [EBNA6_EBVB9] [TCA_HUMAN] [TCB_HUMAN] by SWISSPFAM
  • Domains found in 3DXA: [IG] [IG_like] [IGc1 ] by SMART
  • Other resources with information on 3DXA
  • Community annotation for 3DXA 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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