2DYP Immune System date Sep 15, 2006
title Crystal Structure Of Lilrb2(Lir2ilt4cd85d) Complexed With Hla-G
authors M.Shiroishi, K.Kuroki, L.Rasubala, D.Kohda, K.Maenaka
compound source
Molecule: Hla Class I Histocompatibility Antigen, Alpha Chain G;
Chain: A
Fragment: Residues In Data Base 25-300
Synonym: Hla G Antigen
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: Beta-2-Microglobulin
Chain: B
Fragment: Residues In Data Base 24-219
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: 9 Mer Peptide From Histone H2a.X
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: This Peptide Was Chemically Synthesized

Molecule: Leukocyte Immunoglobulin-Like Receptor Subfamily B Member 2;
Chain: D
Synonym: Leukocyte Immunoglobulin-Like Receptor 2, Lir-2, Immunoglobulin- Like Transcript 4, Ilt-4, Monocytemacrophage Immunoglobulin-Like Receptor 10, Mir- 10, Cd85d Antigen;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7
symmetry Space Group: P 31 2 1
R_factor 0.233 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.400 81.400 186.733 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
Gene
Ontology
ChainFunctionProcessComponent
B
  • cellular response to iron io...

  • Primary referenceStructural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d)., Shiroishi M, Kuroki K, Rasubala L, Tsumoto K, Kumagai I, Kurimoto E, Kato K, Kohda D, Maenaka K, Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16412-7. Epub 2006 Oct 20. PMID:17056715
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk]
  • Biological Unit Coordinates (2dyp.pdb1.gz) 96 Kb
  • CSU: Contacts of Structural Units for 2DYP
  • Likely Quarternary Molecular Structure file(s) for 2DYP
  • Structure Factors (195 Kb)
  • Retrieve 2DYP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DYP from S2C, [Save to disk]
  • Re-refined 2dyp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DYP 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 2DYP
  • 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 2DYP, from MSDmotif at EBI
  • Fold representative 2dyp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dyp_A] [2dyp_B] [2dyp_D] [2dyp] [2dyp_C]
  • SWISS-PROT database: [P61769] [P16104] [P17693] [Q8N423]
  • Domain organization of [B2MG_HUMAN] [H2AX_HUMAN] [HLAG_HUMAN] [LIRB2_HUMAN] by SWISSPFAM
  • Domains found in 2DYP: [IG] [IGc1 ] by SMART
  • Other resources with information on 2DYP
  • Community annotation for 2DYP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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