4GBX Immune System date Jul 28, 2012
title Crystal Structure Of An Immune Complex At Ph 6.5
authors D.K.Sethi, W.Pos, K.W.Wucherpfennig
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dm Alpha
Chain: C
Synonym: Mhc Class II Antigen Dma, Really Interesting New G Protein;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Alpha Chain, Dma, Hla-Dm, Hla-Dma, Mhc Class II Molec Ring6;
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_strain: Lec3.2.8.1
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pee14.1

Molecule: Hla Class II Histocompatibility Antigen, Dm Beta
Chain: D
Synonym: Mhc Class II Antigen Dmb, Really Interesting New G Protein;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Beta Chain, Dmb, Hla-Dmb, Mhc Class II Molecule Hla-D
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_strain: Lec3.2.8.1
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pee14.1

Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Alpha Chain, Hla-Dr1, Hla-Dra, Hla-Dra1, Mhc Class II Molecule;
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 B
Chain: B
Synonym: Mhc Class II Antigen Drb11, Dr-1, Dr1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Beta Chain, Hla-Dr1, Hla-Drb1, Mhc Class II Molecule
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Synthetic Peptide
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_common: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.167 126.032 143.107 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceCrystal Structure of the HLA-DM-HLA-DR1 Complex Defines Mechanisms for Rapid Peptide Selection., Pos W, Sethi DK, Call MJ, Schulze MS, Anders AK, Pyrdol J, Wucherpfennig KW, Cell. 2012 Dec 21;151(7):1557-68. doi: 10.1016/j.cell.2012.11.025. PMID:23260142
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (263 Kb) [Save to disk]
  • Biological Unit Coordinates (4gbx.pdb1.gz) 127 Kb
  • Biological Unit Coordinates (4gbx.pdb2.gz) 129 Kb
  • LPC: Ligand-Protein Contacts for 4GBX
  • CSU: Contacts of Structural Units for 4GBX
  • Structure Factors (194 Kb)
  • Retrieve 4GBX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GBX from S2C, [Save to disk]
  • Re-refined 4gbx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GBX 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 4GBX
  • 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 4GBX, from MSDmotif at EBI
  • Fold representative 4gbx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gbx_E] [4gbx] [4gbx_B] [4gbx_D] [4gbx_C] [4gbx_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4GBX: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 4GBX
  • Community annotation for 4GBX at PDBWiki (http://pdbwiki.org)
  • 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