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
  • Alignments of the sequence of 3ONA with the sequences similar proteins can be viewed for 3ONA'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 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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