OCA Atlas for 1I1Y
1I1Y Immune System date Apr 16, 1999
title Crystal Structure Of Human Class I Mhc (Hla-A2.1) Complexed With Beta 2-Microglobulin And Hiv-Rt Variant Peptide I1y
authors T.J.Kirksey, R.R.Pogue-Caley, J.A.Frelinger, E.J.Collins
compound source
Molecule: Class I Histocompatibility Antigen
Chain: A, D
Fragment: Peptide-Binding Domain + Alpha3
Synonym: Hla-A2.1
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Strain: Bl21 Plyss
Cellular_location: Cytoplasm
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_strain: Bl21 Plyss
Expression_system_cellular_location: Inclusion Bodies
Expression_system_vector_type: Plasmid
Expression_system_vector: E.Coli
Expression_system_plasmid: Plm1

Molecule: Beta 2-Microglobulin
Chain: B, E
Fragment: Beta 2-Microglobulin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Strain: Bl21 Plyss
Cellular_location: Cytoplasm
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_strain: Bl21 Plyss
Expression_system_cellular_location: Inclusion Body
Expression_system_vector_type: Plasmid
Expression_system_vector: E.Coli
Expression_system_plasmid: Plm1

Molecule: Hiv-Rt Variant Peptide I1y (Ylkepvhgv)
Chain: C, F
Fragment: Residues 309-317
Synonym: I1y
Engineered: Yes
Mutation: Yes
Synthetic: Yes
symmetry Space Group: P 1
R_factor 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.613 63.591 75.326 81.93 75.94 78.00
method X-Ray Diffractionresolution 2.2 Å
related structures by homologous chain: 1DUY, 1QR1
similarity Belongs to the MHC_I family.
subunit Dimer of alpha chain and a beta chain (beta-2- microglobulin).
polymorphism The following alleles of a-2 are known a*0202, a*0203, a*0204, a*0205, a*0206 (a2.4a), a*0207, a*0208, a*0209, a*0210, a*0211 (a2.5), a*0212, a*0213 (a*02slu), a*0216, a*0217, a*0218 (a2k), a*0219, a*0220 and a*0221. The sequence shown is that of a*0201.
genes HLA-A, HLAA (H. sapiens)
function Involved in the presentation of foreign antigens to the immune system.
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1I1Y
  • Likely Quarternary Molecular Structure file(s) for 1I1Y
  • Structure Factors (r1i1ysf.ent.Z) 353 Kb
  • Retrieve 1I1Y in mmCIF format [Save to disk]
    • View 1I1Y in 3D
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • FirstGlance in Chemscape Chime (Install Chime freeware) This is good for easiest viewing of basic structure.
  • RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1I1Y
  • STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i1ya2, region A:1-181 [rasmolscript] [script source]
        - Domain d1i1ya1, region A:182-275 [rasmolscript] [script source]
        - Domain d1i1yb1, region B: [rasmolscript] [script source]
        - Domain d1i1yd2, region D:1-181 [rasmolscript] [script source]
        - Domain d1i1yd1, region D:182-275 [rasmolscript] [script source]
        - Domain d1i1ye1, region E: [rasmolscript] [script source]
  • Fold representative 1i1y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily: CATH
  • Summaries and structural analyses of PDB data files: PDBSum
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1i1y_A] [1i1y_B] [1i1y_C] [1i1y_D] [1i1y_E] [1i1y_F]
  • SWISS-PROT database: [1A02_HUMAN]
  • Domain organization of [1A02_HUMAN] by SWISSPFAM
  • Domain found in 1I1Y: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family MHC_I (PF00129) of Pfam.
  • Alignments of the sequence of 1I1Y with the sequences similar proteins can be viewed for classification [1A02_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 [1A02_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1I1Y
  • InterPro: IPR003006 , IPR001039
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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