4GG6 Immune System date Aug 06, 2012
title Protein Complex
authors S.E.Broughton, A.Theodossis, J.Petersen, H.H.Reid, J.Rossjohn
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dq Alpha
Chain: A, C
Fragment: Extracellular Domains, Unp Residues 24-206
Synonym: Dc-1 Alpha Chain, Dc-Alpha, Hla-Dca, Mhc Class II
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dqa1
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_strain: Hi5
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbacdual

Molecule: Hla Class II Histocompatibility Antigen, Dq Beta
Chain: B, D
Fragment: Extracellular Domains, Unp Residues 33-224
Synonym: Mhc Class II Antigen Dqb1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dqb, Hla-Dqb1
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_strain: Hi5
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbacdual

Molecule: T-Cell Receptor, Sp3.4 Alpha Chain
Chain: E, G
Fragment: Extracellular Domains
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet

Molecule: T-Cell Receptor, Sp3.4 Beta Chain
Chain: F, H
Fragment: Extracellular Domains
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet

Molecule: Peptide From Alphabeta-Gliadin Mm1
Chain: I, J
Fragment: Deamidated Alpha-I Gliadin Peptide, Unp Residues
Synonym: Prolamin
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Organism_scientific: Triticum Aestivum
Organism_common: Wheat
Organism_taxid: 4565
Other_details: Chemical Synthesis
symmetry Space Group: P 21 21 21
R_factor 0.246 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.708 134.325 140.304 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceBiased T Cell Receptor Usage Directed against Human Leukocyte Antigen DQ8-Restricted Gliadin Peptides Is Associated with Celiac Disease., Broughton SE, Petersen J, Theodossis A, Scally SW, Loh KL, Thompson A, van Bergen J, Kooy-Winkelaar Y, Henderson KN, Beddoe T, Tye-Din JA, Mannering SI, Purcell AW, McCluskey J, Anderson RP, Koning F, Reid HH, Rossjohn J, Immunity. 2012 Oct 19;37(4):611-21. doi: 10.1016/j.immuni.2012.07.013. Epub 2012 , Oct 11. PMID:23063329
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (424 Kb) [Save to disk]
  • Biological Unit Coordinates (4gg6.pdb1.gz) 206 Kb
  • Biological Unit Coordinates (4gg6.pdb2.gz) 211 Kb
  • LPC: Ligand-Protein Contacts for 4GG6
  • CSU: Contacts of Structural Units for 4GG6
  • Structure Factors (463 Kb)
  • Retrieve 4GG6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GG6 from S2C, [Save to disk]
  • Re-refined 4gg6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GG6 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 4GG6
  • 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 4GG6, from MSDmotif at EBI
  • Fold representative 4gg6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gg6] [4gg6_A] [4gg6_H] [4gg6_E] [4gg6_J] [4gg6_C] [4gg6_G] [4gg6_F] [4gg6_D] [4gg6_I] [4gg6_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4GG6: [IG] [IGc1] [IGv] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 4GG6
  • Community annotation for 4GG6 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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