3VHT Fluorescent Protein Protein Binding date Sep 06, 2011
title Crystal Structure Of Gfp-Wrnip1 Ubz Domain Fusion Protein In With Ubiquitin
authors N.Suzuki, S.Wakatsuki, M.Kawasaki
compound source
Molecule: Green Fluorescent Protein
Chain: A
Fragment: Gfp Domain
Engineered: Yes
Organism_scientific: Aequorea Victoria
Organism_common: Jellyfish
Organism_taxid: 6100
Gene: Gfp
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: Green Fluorescent Protein,Atpase Wrnip1
Chain: B
Fragment: Gfp,Wrnip1 Ubz Domain (Unp Residues 9-46)
Synonym: Werner Helicase-Interacting Protein 1
Ec: 3.6.1.3
Engineered: Yes
Other_details: The Fusion Protein Of Yeast Enhanced Green F Protein, Linker (Gly-Ser) And Human Wrnip1 Ubz;

Organism_scientific: Aequorea Victoria, Homo Sapiens
Organism_common: Jellyfish, Human
Organism_taxid: 6100, 9606
Gene: Gfp, Wrnip1, Whip
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: Ubiquitin
Chain: C

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
symmetry Space Group: C 2 2 21
R_factor 0.191 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.950 143.692 106.864 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CR2, ZN enzyme Hydrolase E.C.3.6.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceA novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1., Suzuki N, Rohaim A, Kato R, Dikic I, Wakatsuki S, Kawasaki M, FEBS J. 2016 Apr 8. doi: 10.1111/febs.13734. PMID:27062441
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (192 Kb) [Save to disk]
  • Biological Unit Coordinates (3vht.pdb1.gz) 186 Kb
  • LPC: Ligand-Protein Contacts for 3VHT
  • CSU: Contacts of Structural Units for 3VHT
  • Structure Factors (420 Kb)
  • Retrieve 3VHT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VHT from S2C, [Save to disk]
  • Re-refined 3vht structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VHT 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 3VHT
  • 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
  • 3D motif for 3VHT, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vht_C] [3vht_B] [3vht] [3vht_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3VHT: [UBQ] [ZnF_Rad18 ] by SMART
  • Other resources with information on 3VHT
  • Community annotation for 3VHT at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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