4P4K Immune System date Mar 12, 2014
title Structural Basis Of Chronic Beryllium Disease: Bridging The Between Allergic Hypersensitivity And Auto Immunity
authors G.M.Clayton, F.Crawford, J.W.Kappler
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dp Alpha
Chain: A, E
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: Unidentified Baculovirus
Expression_system_taxid: 10469
Expression_system_strain: Bti Tn 5b1 4

Molecule: Mim2 Peptide,Hla Class II Histocompatibility Anti Beta 1 Chain;
Chain: B, F
Fragment: Unp Residues 32-218
Synonym: Hla Class II Histocompatibility Antigen,Dp(W4) Bet Mhc Class II Antigen Dpb1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dpb1, Hla-Dp1b
Expression_system: Unidentified Baculovirus
Expression_system_taxid: 10469

Molecule: Htcrav22 Alpha Chain
Chain: C, G
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Htcrav22 Beta Chain
Chain: D, H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.204 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.400 137.240 213.130 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 0BE, NA, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, 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] (278 Kb) [Save to disk]
  • Biological Unit Coordinates (4p4k.pdb1.gz) 138 Kb
  • Biological Unit Coordinates (4p4k.pdb2.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 4P4K
  • CSU: Contacts of Structural Units for 4P4K
  • Structure Factors (448 Kb)
  • Retrieve 4P4K in mmCIF format [Save to disk]
  • Re-refined 4p4k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4P4K 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 4P4K
  • 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 4P4K, from MSDmotif at EBI
  • Fold representative 4p4k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p4k_B] [4p4k_H] [4p4k_D] [4p4k_E] [4p4k_A] [4p4k_F] [4p4k] [4p4k_G] [4p4k_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4P4K: [IG] [IG_like] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 4P4K
  • Community annotation for 4P4K at PDBWiki (http://pdbwiki.org)

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