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 Diffraction	resolution	3.40 Å
Gene Ontology	Chain Function Process Component D, B protein binding positive regulation of T cel... response to molecule of bact... antigen processing and prese... antigen processing and prese... antigen processing and prese... antigen processing and prese... immune response viral reproduction cytokine-mediated signaling ... T cell differentiation in th... protein refolding response to drug antigen processing and prese... innate immune response response to cadmium ion regulation of defense respon... regulation of immune respons... interferon-gamma-mediated si... Golgi membrane extracellular region extracellular space endoplasmic reticulum lumen plasma membrane external side of plasma memb... ER to Golgi transport vesicl... phagocytic vesicle membrane early endosome membrane early endosome lumen MHC class I protein complex
Primary reference	CD94-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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [3cdg_B] [3cdg_C] [3cdg_D] [3cdg_E] [3cdg_F] [3cdg_J] [3cdg_K] [3cdg_P] [3cdg_Q] 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)

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