3ONA Viral Protein Cytokine date Aug 28, 2010
title The Secret Domain In Complex With Cx3cl1
authors X.Q.Wang, X.G.Xue, D.L.Wang
compound source
Molecule: Tumour Necrosis Factor Receptor
Chain: A
Fragment: Secret Domain, Unp Residues 162-320
Engineered: Yes
Organism_scientific: Ectromelia Virus
Organism_taxid: 12643
Gene: Crmd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Cx3cl1 Protein
Chain: B
Fragment: Chemokine Domain, Unp Residues 24-100
Synonym: Cx3cl1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: P 32 2 1
R_factor 0.196 R_Free 0.250
length a length b length c angle alpha angle beta angle gamma
71.330 71.330 93.141 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å

Primary referenceStructural basis of chemokine sequestration by CrmD, a poxvirus-encoded tumor necrosis factor receptor., Xue X, Lu Q, Wei H, Wang D, Chen D, He G, Huang L, Wang H, Wang X, PLoS Pathog. 2011 Jul;7(7):e1002162. Epub 2011 Jul 28. PMID:21829356
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (3ona.pdb1.gz) 76 Kb
  • CSU: Contacts of Structural Units for 3ONA
  • Structure Factors (116 Kb)
  • Retrieve 3ONA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ONA from S2C, [Save to disk]
  • Re-refined 3ona structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ONA 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 3ONA
  • 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 3ONA, from MSDmotif at EBI
  • Fold representative 3ona from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ona_A] [3ona] [3ona_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ONA: [SCY ] by SMART
  • Other resources with information on 3ONA
  • Community annotation for 3ONA at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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