4P5K Immune System date Mar 17, 2014
title Structural Basis Of Chronic Beryllium Disease: Bridging The Between Allergy And Autoimmunity
authors G.M.Clayton, Y.Wang, F.Crawford, A.Novikov, B.T.Wimberly, J.S.Kie M.T.Falta, N.A.Bowerman, P.Marrack, A.P.Fontenot, S.Dai, J.W.Kap
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dp Alpha
Chain: A, D
Fragment: Unp Residues 32-214
Synonym: Dp(W3),Dp(W4),Hla-Sb Alpha Chain,Mhc Class II Dp3- Class II Dpa1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dpa1, Hla-Dp1a, Hlasb
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Ras Peptide,Hla Class II Histocompatibility Antig Beta 1 Chain;
Chain: B, E
Fragment: Unp Residues 32-218
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dpb1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: C 1 2 1
R_factor 0.221 R_Free 0.281
length a length b length c angle alpha angle beta angle gamma
182.779 68.738 71.133 90.00 105.72 90.00
method X-Ray Diffractionresolution 2.59 Å
A, D

E, B

Primary referenceStructural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity., Clayton GM, Wang Y, Crawford F, Novikov A, Wimberly BT, Kieft JS, Falta MT, Bowerman NA, Marrack P, Fontenot AP, Dai S, Kappler JW, Cell. 2014 Jul 3;158(1):132-42. doi: 10.1016/j.cell.2014.04.048. PMID:24995984
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (261 Kb) [Save to disk]
  • Biological Unit Coordinates (4p5k.pdb1.gz) 129 Kb
  • Biological Unit Coordinates (4p5k.pdb2.gz) 128 Kb
  • CSU: Contacts of Structural Units for 4P5K
  • Structure Factors (487 Kb)
  • Retrieve 4P5K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P5K from S2C, [Save to disk]
  • Re-refined 4p5k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4P5K 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 4P5K
  • 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 4P5K, from MSDmotif at EBI
  • Fold representative 4p5k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p5k_D] [4p5k_B] [4p5k_E] [4p5k] [4p5k_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4P5K: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 4P5K
  • Community annotation for 4P5K at PDBWiki (http://pdbwiki.org)

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