3CL3 Viral Protein Signaling Protein date Mar 18, 2008
title Crystal Structure Of A Vflip-Ikkgamma Complex: Insights Into Viral Activation Of The Ikk Signalosome
authors C.Bagneris, A.V.Ageichik, N.Cronin, C.Boshoff, G.Waksman, T.Barrett
compound source
Molecule: Orf K13
Chain: A, B
Fragment: Residues 1-178
Synonym: Ks-Vflip
Engineered: Yes
Organism_scientific: Human Herpesvirus 8
Strain: Na
Gene: Vflip
Expression_system: Escherichia Coli
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm442

Molecule: Nf-Kappa-B Essential Modulator
Chain: D, E
Fragment: Residues 150-272
Synonym: Nemo, Nf-Kappa-B Essential Modifier, Inhibitor Of Nuclear Factor Kappa-B Kinase Subunit Gamma, Ikb Kinase Subunit Gamma, I-Kappa-B Kinase Gamma, Ikk-Gamma, Ikkg, Ikb Kinase-Associated Protein 1, Ikkap1, Fip-3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Gene: Ikbkg, Fip3, Nemo
Expression_system: Escherichia Coli
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm6t1
symmetry Space Group: P 32 2 1
R_factor 0.261 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
145.670 145.670 101.540 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.20 Å
Primary referenceCrystal structure of a vFlip-IKKgamma complex: insights into viral activation of the IKK signalosome., Bagneris C, Ageichik AV, Cronin N, Wallace B, Collins M, Boshoff C, Waksman G, Barrett T, Mol Cell. 2008 Jun 6;30(5):620-31. PMID:18538660
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3cl3.pdb1.gz) 71 Kb
  • CSU: Contacts of Structural Units for 3CL3
  • Likely Quarternary Molecular Structure file(s) for 3CL3
  • Structure Factors (159 Kb)
  • Retrieve 3CL3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CL3 from S2C, [Save to disk]
  • Re-refined 3cl3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CL3 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 3CL3
  • 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 3CL3, from MSDmotif at EBI
  • Fold representative 3cl3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cl3_D] [3cl3_A] [3cl3_B] [3cl3] [3cl3_E]
  • SWISS-PROT database: [Q9Y6K9] [Q76RF1]
  • Domain organization of [NEMO_HUMAN] [Q76RF1_HHV8] by SWISSPFAM
  • Domain found in 3CL3: [DED ] by SMART
  • Alignments of the sequence of 3CL3 with the sequences similar proteins can be viewed for 3CL3's classification [NEMO_HUMAN] [Q76RF1_HHV8] 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 [NEMO_HUMAN] [Q76RF1_HHV8] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3CL3
  • Community annotation for 3CL3 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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