4I9X Apoptosis date Dec 05, 2012
title Crystal Structure Of Human Cytomegalovirus Glycoprotein Ul14 Targeting The Death Receptor Trail-R2
authors I.Nemcovicova, D.M.Zajonc
compound source
Molecule: Protein Ul141
Chain: A, B
Fragment: Ul141, Unp Residues 32-246
Engineered: Yes
Organism_scientific: Human Herpesvirus 5
Organism_common: Hhv-5
Organism_taxid: 295027
Strain: Merlin
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: C, D
Fragment: Trail-R2, Unp Residues 58-184
Synonym: Death Receptor 5, Tnf-Related Apoptosis-Inducing L Receptor 2, Trail Receptor 2, Trail-R2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.916 97.043 141.422 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA, MSE, NA, NAG enzyme
Primary referenceStructure of Human Cytomegalovirus UL141 Binding to TRAIL-R2 Reveals Novel, Non-canonical Death Receptor Interactions., Nemcovicova I, Benedict CA, Zajonc DM, PLoS Pathog. 2013 Mar;9(3):e1003224. doi: 10.1371/journal.ppat.1003224. Epub 2013, Mar 21. PMID:23555243
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (4i9x.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 4I9X
  • CSU: Contacts of Structural Units for 4I9X
  • Structure Factors (769 Kb)
  • Retrieve 4I9X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4I9X from S2C, [Save to disk]
  • Re-refined 4i9x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4I9X 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 4I9X
  • 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 4I9X, from MSDmotif at EBI
  • Fold representative 4i9x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4i9x] [4i9x_C] [4i9x_B] [4i9x_A] [4i9x_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4I9X: [IG] [TNFR ] by SMART
  • Other resources with information on 4I9X
  • Community annotation for 4I9X at PDBWiki (http://pdbwiki.org)

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