3VTV Protein Binding date Jun 08, 2012
title Crystal Structure Of Optineurin Lir-Fused Human Lc3b_2-119
authors H.Suzuki, M.Kawasaki, R.Kato, S.Wakatsuki
compound source
Molecule: Optineurin, Microtubule-Associated Proteins 1a1b Chain 3b;
Chain: A
Fragment: Unp Residues 170-181, Residues 2-119
Synonym: Autophagy-Related Protein Lc3 B, Autophagy-Related Ubiquitin-Like Modifier Lc3 B, Map1 Light Chain 3-Like Prot Map1amap1b Light Chain 3 B, Map1amap1b Lc3 B, Microtubule Associated Protein 1 Light Chain 3 Beta;
Engineered: Yes
Mutation: Yes
Other_details: The Fusion Protein Of Optineurin Lir (Residu 181) And Microtubule-Associated Proteins 1a1b Light Chain (Residues 2-119)
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map1lc3b, Map1alc3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t-1
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.252
length a length b length c angle alpha angle beta angle gamma
35.200 53.000 60.960 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand SO4 enzyme

Primary referenceStructural basis for phosphorylation-triggered autophagic clearance of Salmonella., Rogov VV, Suzuki H, Fiskin E, Wild P, Kniss A, Rozenknop A, Kato R, Kawasaki M, McEwan DG, Lohr F, Guntert P, Dikic I, Wakatsuki S, Dotsch V, Biochem J. 2013 Jun 28. PMID:23805866
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (3vtv.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 3VTV
  • CSU: Contacts of Structural Units for 3VTV
  • Structure Factors (182 Kb)
  • Retrieve 3VTV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VTV from S2C, [Save to disk]
  • Re-refined 3vtv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VTV 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 3VTV
  • 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 3VTV, from MSDmotif at EBI
  • Fold representative 3vtv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vtv_A] [3vtv]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VTV
  • Community annotation for 3VTV at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science