2BNQ Immune System Receptor date Mar 31, 2005
title Structural And Kinetic Basis For Heightened Immunogenicity Of T Cell Vaccines
authors J.L.Chen, G.Stewart-Jones, G.Bossi, N.M.Lissin, L.Wooldridge, E.M.L.Choi, G.Held, P.R.Dunbar, R.M.Esnouf, M.Sami, J.M.Boultier, P.Rizkallah, C.Renner, A.Sewell, P.A.Van Der Merwe, B.K.Jackobsen, G.Griffiths, E.Y.Jones, V.Cerundolo
compound source
Molecule: Hla Class I Histocompatibility Antigen
Chain: A
Fragment: Extracellular Alpha-1, -2, -3, Residues 25-300
Synonym: Mhc, A-2 Alpha Chain Precursor
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Antigen Presenting Cell
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr
Expression_system_vector: Pett22b+
Other_details: Refolded From Inclusion Bodies

Molecule: Beta-2-Microglobulin
Chain: B
Fragment: Beta-2-Microglobulin, Residues 21-119
Synonym: Hdcma22p, B2m
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Antigen Presenting Cell
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr
Expression_system_vector: Pett22b+
Other_details: Refolded From Inclusion Bodies From Inclusion Bodies;

Molecule: Synthetic Peptide
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Antigen Presenting Cell
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr
Expression_system_vector: Pett22b+
Other_details: Refolded From Inclusion Bodies. Peptide Chain C.;

Molecule: T-Cell Receptor Alpha Chain V Region
Chain: D
Engineered: Yes
Other_details: Contains Also C (Constant) Region

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Immune Sytem
Cell: T-Lymphocyte
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr
Expression_system_vector: Pett22b+
Other_details: Refolded From Inclusion Bodies

Molecule: T-Cell Receptor Beta Chain C Region
Chain: E
Fragment: Extracellular, Residues 1-130
Synonym: Trbc1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Immune Sytem
Cell: T-Lymphocyte
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr
Expression_system_vector: Pett22b+
Other_details: Refolded From Inclusion Bodies.
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.563 62.490 116.955 90.00 105.34 90.00
method X-Ray Diffractionresolution 1.7 Å
related structures by homologous chain: 1BEC, 1KGC, 1N2R, 1ZSD, 2BNR
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural and kinetic basis for heightened immunogenicity of T cell vaccines., Chen JL, Stewart-Jones G, Bossi G, Lissin NM, Wooldridge L, Choi EM, Held G, Dunbar PR, Esnouf RM, Sami M, Boulter JM, Rizkallah P, Renner C, Sewell A, van der Merwe PA, Jakobsen BK, Griffiths G, Jones EY, Cerundolo V, J Exp Med. 2005 Apr 18;201(8):1243-55. PMID:15837811
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (2bnq.pdb1.gz) 146 Kb
  • CSU: Contacts of Structural Units for 2BNQ
  • Likely Quarternary Molecular Structure file(s) for 2BNQ
  • Structure Factors (816 Kb)
  • Retrieve 2BNQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BNQ from S2C, [Save to disk]
  • Re-refined 2bnq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BNQ 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 2BNQ
  • 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 2BNQ, from MSDmotif at EBI
  • Fold representative 2bnq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bnq_C] [2bnq_D] [2bnq_B] [2bnq_E] [2bnq_A] [2bnq]
  • SWISS-PROT database: [P01892] [P61769] [P78358] [P01848] [P01850]
  • Domain organization of [1A02_HUMAN] [B2MG_HUMAN] [CTG1B_HUMAN] [TCA_HUMAN] [TCB_HUMAN] by SWISSPFAM
  • Domains found in 2BNQ: [IG_like] [IGc1] [IGv ] by SMART
  • Alignments of the sequence of 2BNQ with the sequences similar proteins can be viewed for 2BNQ's classification [1A02_HUMAN] [B2MG_HUMAN] [CTG1B_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 [1A02_HUMAN] [B2MG_HUMAN] [CTG1B_HUMAN] [TCA_HUMAN] [TCB_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2BNQ
  • Community annotation for 2BNQ 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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