3B13 Protein Binding Signaling Protein date Jun 24, 2011
title Crystal Structure Of The Dhr-2 Domain Of Dock2 In Complex Wi (T17n Mutant)
authors K.Hanawa-Suetsugu, M.Kukimoto-Niino, C.Mishima-Tsumagari, T.Ter M.Shirouzu, Y.Fukui, S.Yokoyama
compound source
Molecule: Dedicator Of Cytokinesis Protein 2
Chain: A, C
Fragment: Dhr-2 Domain (Unp Residues 1196-1622)
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dock2, Kiaa0209
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pe100108-03

Molecule: Ras-Related C3 Botulinum Toxin Substrate 1
Chain: B, D
Fragment: Gtpase Domain (Unp Residues 1-177)
Synonym: Cell Migration-Inducing Gene 5 Protein, Ras-Like P Tc25, P21-Rac1;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rac1, Tc25, Mig5
Expression_system: Cell-Free Synthesis
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Px080214-11
symmetry Space Group: P 65
R_factor 0.183 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
168.651 168.651 129.718 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.01 Å
Gene
Ontology
ChainFunctionProcessComponent
D, B


Primary referenceStructural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms., Hanawa-Suetsugu K, Kukimoto-Niino M, Mishima-Tsumagari C, Akasaka R, Ohsawa N, Sekine S, Ito T, Tochio N, Koshiba S, Kigawa T, Terada T, Shirouzu M, Nishikimi A, Uruno T, Katakai T, Kinashi T, Kohda D, Fukui Y, Yokoyama S, Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3305-10. Epub 2012 Feb 13. PMID:22331897
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (422 Kb) [Save to disk]
  • Biological Unit Coordinates (3b13.pdb1.gz) 414 Kb
  • CSU: Contacts of Structural Units for 3B13
  • Structure Factors (342 Kb)
  • Retrieve 3B13 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B13 from S2C, [Save to disk]
  • Re-refined 3b13 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3B13 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 3B13
  • 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 3B13, from MSDmotif at EBI
  • Fold representative 3b13 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b13_A] [3b13_B] [3b13] [3b13_C] [3b13_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3B13: [RHO ] by SMART
  • Other resources with information on 3B13
  • Community annotation for 3B13 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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