3A98

Crystal structure of the complex of the interacting regions of DOCK2 and ELMO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural 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.

(2012) Proc Natl Acad Sci U S A 109: 3305-3310

  • DOI: 10.1073/pnas.1113512109
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • DOCK2, a hematopoietic cell-specific, atypical guanine nucleotide exchange factor, controls lymphocyte migration through ras-related C3 botulinum toxin substrate (Rac) activation. Dedicator of cytokinesis 2-engulfment and cell motility protein 1 (DOC ...

    DOCK2, a hematopoietic cell-specific, atypical guanine nucleotide exchange factor, controls lymphocyte migration through ras-related C3 botulinum toxin substrate (Rac) activation. Dedicator of cytokinesis 2-engulfment and cell motility protein 1 (DOCK2•ELMO1) complex formation is required for DOCK2-mediated Rac signaling. In this study, we identified the N-terminal 177-residue fragment and the C-terminal 196-residue fragment of human DOCK2 and ELMO1, respectively, as the mutual binding regions, and solved the crystal structure of their complex at 2.1-Å resolution. The C-terminal Pro-rich tail of ELMO1 winds around the Src-homology 3 domain of DOCK2, and an intermolecular five-helix bundle is formed. Overall, the entire regions of both DOCK2 and ELMO1 assemble to create a rigid structure, which is required for the DOCK2•ELMO1 binding, as revealed by mutagenesis. Intriguingly, the DOCK2•ELMO1 interface hydrophobically buries a residue which, when mutated, reportedly relieves DOCK180 from autoinhibition. We demonstrated that the ELMO-interacting region and the DOCK-homology region 2 guanine nucleotide exchange factor domain of DOCK2 associate with each other for the autoinhibition, and that the assembly with ELMO1 weakens the interaction, relieving DOCK2 from the autoinhibition. The interactions between the N- and C-terminal regions of ELMO1 reportedly cause its autoinhibition, and binding with a DOCK protein relieves the autoinhibition for ras homolog gene family, member G binding and membrane localization. In fact, the DOCK2•ELMO1 interface also buries the ELMO1 residues required for the autoinhibition within the hydrophobic core of the helix bundle. Therefore, the present complex structure reveals the structural basis by which DOCK2 and ELMO1 mutually relieve their autoinhibition for the activation of Rac1 for lymphocyte chemotaxis.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dedicator of cytokinesis protein 2
A, C
184Homo sapiensMutation(s): 0 
Gene Names: DOCK2KIAA0209
Find proteins for Q92608 (Homo sapiens)
Go to UniProtKB:  Q92608
NIH Common Fund Data Resources
PHAROS  Q92608

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Engulfment and cell motility protein 1
B, D
203Homo sapiensMutation(s): 0 
Gene Names: ELMO1KIAA0281
Find proteins for Q92556 (Homo sapiens)
Go to UniProtKB:  Q92556
NIH Common Fund Data Resources
PHAROS  Q92556
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,C, B,D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.837α = 90
b = 104.028β = 90
c = 124.731γ = 90
Software Package:
Software NamePurpose
autoSHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references, Derived calculations