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
  • Alignments of the sequence of 4GG6 with the sequences similar proteins can be viewed for 4GG6's classification 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 at ProtoMap. Click on the Cluster number.
  • 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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