3CDG Immune System date Feb 26, 2008
title Human Cd94nkg2a In Complex With Hla-E
authors E.J.Petrie, C.S.Clements, J.Lin, L.C.Sullivan, D.Johnson, T.Huyton, A.Heroux, H.L.Hoare, T.Beddoe, H.H.Reid, M.C.J.Wilce, A.G.Brooks, J.Rossjohn
compound source
Molecule: Hla Class I Histocompatibility Antigen, Alpha Chain E;
Chain: A, C
Fragment: Residues In Database 23-295
Synonym: Mhc Class I Antigen E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-E, Hla-6.2, Hlae
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Beta-2-Microglobulin
Chain: B, D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Natural Killer Cells Antigen Cd94
Chain: J, E
Fragment: Residues In Database 57-179
Synonym: Nk Cell Receptor, Killer Cell Lectin-Like Receptor Subfamily D Member 1, Kp43;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Klrd1, Cd94
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Nkg2-Ankg2-B Type II Integral Membrane Protein
Chain: K, F
Fragment: Residues In Database 113-232
Synonym: Nkg2-Ab-Activating Nk Receptor, Nk Cell Receptor A, Cd159a Antigen;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Klrc1, Nkg2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Leader Peptide Of Hla Class I Histocompatibility Antigen, Alpha Chain G;
Chain: P, Q
Synonym: Hla G Antigen
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Of The Human Hla-G Leader Sequence
symmetry Space Group: I 41 3 2
R_factor 0.249 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
345.201 345.201 345.201 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
Gene
Ontology
ChainFunctionProcessComponent
D, B


Primary referenceCD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence., Petrie EJ, Clements CS, Lin J, Sullivan LC, Johnson D, Huyton T, Heroux A, Hoare HL, Beddoe T, Reid HH, Wilce MC, Brooks AG, Rossjohn J, J Exp Med. 2008 Mar 17;205(3):725-35. Epub 2008 Mar 10. PMID:18332182
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (219 Kb) [Save to disk]
  • Biological Unit Coordinates (3cdg.pdb1.gz) 107 Kb
  • Biological Unit Coordinates (3cdg.pdb2.gz) 108 Kb
  • CSU: Contacts of Structural Units for 3CDG
  • Likely Quarternary Molecular Structure file(s) for 3CDG
  • Structure Factors (445 Kb)
  • Retrieve 3CDG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CDG from S2C, [Save to disk]
  • Re-refined 3cdg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CDG 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 3CDG
  • 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 3CDG, from MSDmotif at EBI
  • Fold representative 3cdg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cdg_Q] [3cdg_D] [3cdg_F] [3cdg_E] [3cdg_K] [3cdg_C] [3cdg_P] [3cdg_B] [3cdg_A] [3cdg_J] [3cdg]
  • SWISS-PROT database: [P61769] [P13747] [P17693] [Q13241] [P26715]
  • Domain organization of [B2MG_HUMAN] [HLAE_HUMAN] [HLAG_HUMAN] [KLRD1_HUMAN] [NKG2A_HUMAN] by SWISSPFAM
  • Domains found in 3CDG: [CLECT] [IGc1 ] by SMART
  • Alignments of the sequence of 3CDG with the sequences similar proteins can be viewed for 3CDG's classification [B2MG_HUMAN] [HLAE_HUMAN] [HLAG_HUMAN] [KLRD1_HUMAN] [NKG2A_HUMAN] 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 [B2MG_HUMAN] [HLAE_HUMAN] [HLAG_HUMAN] [KLRD1_HUMAN] [NKG2A_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3CDG
  • Community annotation for 3CDG 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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