1Y6N Immune System date Dec 06, 2004
title Crystal Structure Of Epstein-Barr Virus Il-10 Mutant (A87i) Complexed With The Soluble Il-10r1 Chain
authors S.I.Yoon, B.C.Jones, N.J.Logsdon, M.R.Walter
compound source
Molecule: Viral Interleukin-10 Homolog
Chain: L
Fragment: Residues 26-170
Synonym: Vil-10, Bcrf1 Protein, 20 Kda Protein
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Herpesvirus 4
Organism_common: Epstein-Barr Virus
Organism_taxid: 10376
Strain: Gd1
Gene: Bcrf1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-32

Molecule: Interleukin-10 Receptor Alpha Chain
Chain: R
Fragment: Extracellular Domain, Residues 22-235
Synonym: Il-10r-A, Il-10r1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il10ra, Il10r
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_cell_line: Schneider Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmtv5his
symmetry Space Group: P 32 1 2
R_factor 0.206 R_Free 0.271
length a length b length c angle alpha angle beta angle gamma
45.603 45.603 310.611 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand MSE enzyme
related structures by homologous chain: 1INR, 1LQS, 1Y6M
  • cytokine activity

  • Primary referenceSame structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain., Yoon SI, Jones BC, Logsdon NJ, Walter MR, Structure (Camb) 2005 Apr;13(4):551-64. PMID:15837194
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (1y6n.pdb1.gz) 115 Kb
  • LPC: Ligand-Protein Contacts for 1Y6N
  • CSU: Contacts of Structural Units for 1Y6N
  • Likely Quarternary Molecular Structure file(s) for 1Y6N
  • Structure Factors (91 Kb)
  • Retrieve 1Y6N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y6N from S2C, [Save to disk]
  • Re-refined 1y6n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y6N 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 1Y6N
  • 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 1Y6N, from MSDmotif at EBI
  • Fold representative 1y6n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y6n] [1y6n_R] [1y6n_L]
  • SWISS-PROT database: [Q13651] [P03180]
  • Domain organization of [I10R1_HUMAN] [IL10H_EBVB9] by SWISSPFAM
  • Domain found in 1Y6N: [IL10 ] by SMART
  • Other resources with information on 1Y6N
  • Community annotation for 1Y6N 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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