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
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
  • Alignments of the sequence of 4I9X with the sequences similar proteins can be viewed for 4I9X's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4I9X
  • Community annotation for 4I9X at PDBWiki (http://pdbwiki.org)

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