Cited by 59Protein Kinase Regulation and GTPase SignalingCellular transport and secretionReceptor Mechanisms and Signaling

Structure of the DOCK2−ELMO1 complex provides insights into regulation of the auto-inhibited state

Open access
Chang, Leifu, Yang, Jing, Jo, Chang Hwa, Boland, Andreas, Zhang, Ziguo, McLaughlin, Stephen H., Abu-Thuraia, Afnan, Killoran, Ryan C. +3 more·2020·Nature Communications

Abstract

DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCK DHR2) and membrane-associated (DOCK DHR1) domains. The structurally-related DOCK1 and DOCK2 GEFs are specific for RAC, and require ELMO (engulfment and cell motility) proteins for function. The N-terminal RAS-binding domain (RBD) of ELMO (ELMO RBD) interacts with RHOG to modulate DOCK1/2 activity. Here, we determine the cryo-EM structures of DOCK2−ELMO1 alone, and as a ternary complex with RAC1, together with the crystal structure of a RHOG−ELMO2 RBD complex. The binary DOCK2−ELMO1 complex adopts a closed, auto-inhibited conformation. Relief of auto-inhibition to an active, open state, due to a conformational change of the ELMO1 subunit, exposes binding sites for RAC1 on DOCK2 DHR2, and RHOG and BAI GPCRs on ELMO1. Our structure explains how up-stream effectors, including DOCK2 and ELMO1 phosphorylation, destabilise the auto-inhibited state to promote an active GEF.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-020-17271-9

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • A recent cryo-electron microscopy structure of the full-length DOCK2-RAC1-ELMO1 complex is consistent with prior predictions and provides the first high-resolution view of conformational and phosphorylation events leading to activation of the complete complex.

    “A recent cryo-electron microscopy-derived structure of this signaling complex using the full-length proteins is consistent with these predictions and provides the first high-resolution view of the conformational and phosphorylation events leading to activation of the complete complex (Fig. 3) (38).”

    From RHO to the DOCK for GDP disembarking: Structural insights into the DOCK GTPase nucleotide exchange factors (2021) · cites this paper as [38]

    Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

    Experimental — accuracy not yet measured
  • The DOCK-C subfamily has dual binding capability, activating both CDC42 and RAC1, except DOCK8, which appears to be a specific CDC42 GEF.

    “The DOCK-C subfamily has dual binding capability, activating both CDC42 and RAC1, except for DOCK8, which appears to be a specific CDC42 GEF (38).”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 71

  1. [1]Heasman SJ Ridley AJ Mammalian Rho GTPases: new insights into their functions from in vivo studies Nat. Rev. Mol. Cell Biol. 2008 9 690 701 18719708
  2. [2]Bagci H Mapping the proximity interaction network of the Rho-family GTPases reveals signalling pathways and regulatory mechanisms Nat. Cell Biol. 2020 22 120 134 31871319
  3. [3]Bos JL Rehmann H Wittinghofer A GEFs and GAPs: critical elements in the control of small G proteins Cell 2007 129 865 877 17540168
  4. [4]Rossman KL Der CJ Sondek J GEF means go: turning on RHO GTPases with guanine nucleotide-exchange factors Nat. Rev. Mol. Cell Biol. 2005 6 167 180 15688002
  5. [5]Vetter IR Wittinghofer A The guanine nucleotide-binding switch in three dimensions Science 2001 294 1299 1304 11701921
  6. [6]Laurin M Cote JF Insights into the biological functions of Dock family guanine nucleotide exchange factors Genes Dev. 2014 28 533 547 24637113 PMC3967044
  7. [7]Cote JF Vuori K GEF what? Dock180 and related proteins help Rac to polarize cells in new ways Trends Cell Biol. 2007 17 383 393 17765544 PMC2887429
  8. [8]Gadea G Blangy A Dock-family exchange factors in cell migration and disease Eur. J. Cell Biol. 2014 93 466 477 25022758
  9. [9]Gadea G Sanz-Moreno V Self A Godi A Marshall CJ DOCK10-mediated Cdc42 activation is necessary for amoeboid invasion of melanoma cells Curr. Biol. 2008 18 1456 1465 18835169
  10. [10]Meller N Merlot S Guda C CZH proteins: a new family of Rho-GEFs J. Cell Sci. 2005 118 4937 4946 16254241
  11. [11]Sanz-Moreno V Rac activation and inactivation control plasticity of tumor cell movement Cell 2008 135 510 523 18984162
  12. [13]Cote JF Vuori K Identification of an evolutionarily conserved superfamily of DOCK180-related proteins with guanine nucleotide exchange activity J. Cell Sci. 2002 115 4901 4913 12432077
  13. [14]Cote JF Vuori K In vitro guanine nucleotide exchange activity of DHR-2/DOCKER/CZH2 domains Methods Enzymol. 2006 406 41 57 16472648
  14. [16]Jaudon F The RhoGEF DOCK10 is essential for dendritic spine morphogenesis Mol. Biol. Cell 2015 26 2112 2127 25851601 PMC4472020
  15. [17]Miyamoto Y Yamauchi J Sanbe A Tanoue A Dock6, a Dock-C subfamily guanine nucleotide exchanger, has the dual specificity for Rac1 and Cdc42 and regulates neurite outgrowth Exp. Cell Res. 2007 313 791 804 17196961
  16. [18]Yamauchi J Miyamoto Y Chan JR Tanoue A ErbB2 directly activates the exchange factor Dock7 to promote Schwann cell migration J. Cell Biol. 2008 181 351 365 18426980 PMC2315680
  17. [19]Yamauchi J The atypical Guanine-nucleotide exchange factor, dock7, negatively regulates schwann cell differentiation and myelination The J. Neurosci. Off. J. Soc. Neurosci. 2011 31 12579 12592 PMC6703263 21880919
  18. [20]Kukimoto-Niino M Structural basis for the dual substrate specificity of DOCK7 guanine nucleotide exchange factor Structure 2019 27 741 748 e743 30853411
  19. [21]Harada Y DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses Blood 2012 119 4451 4461 22461490 PMC3418773
  20. [22]Cote JF Motoyama AB Bush JA Vuori K A novel and evolutionarily conserved PtdIns(3,4,5)P3-binding domain is necessary for DOCK180 signalling Nat. Cell Biol. 2005 7 797 807 16025104 PMC1352170
  21. [23]Premkumar L Structural basis of membrane targeting by the Dock180 family of Rho family guanine exchange factors (Rho-GEFs) J. Biol. Chem. 2010 285 13211 13222 20167601 PMC2857062
  22. [24]Hasegawa H DOCK180, a major CRK-binding protein, alters cell morphology upon translocation to the cell membrane Mol. Cell Biol. 1996 16 1770 1776 8657152 PMC231163
  23. [25]Kiyokawa E Activation of Rac1 by a Crk SH3-binding protein, DOCK180 Genes Dev. 1998 12 3331 3336 9808620 PMC317231
  24. [26]Gumienny TL CED-12/ELMO, a novel member of the CrkII/Dock180/Rac pathway, is required for phagocytosis and cell migration Cell 2001 107 27 41 11595183
  25. [27]Wu YC Tsai MC Cheng LC Chou CJ Weng NYC Elegans CED-12 acts in the conserved crkII/DOCK180/Rac pathway to control cell migration and cell corpse engulfment Dev. Cell 2001 1 491 502 11703940
  26. [28]Zhou Z Caron E Hartwieg E Hall A Horvitz HR The C. elegans PH domain protein CED-12 regulates cytoskeletal reorganization via a Rho/Rac GTPase signaling pathway Dev. Cell 2001 1 477 489 11703939
  27. [29]Sanui T DOCK2 regulates Rac activation and cytoskeletal reorganization through interaction with ELMO1 Blood 2003 102 2948 2950 12829596
  28. [30]Komander D An alpha-helical extension of the ELMO1 pleckstrin homology domain mediates direct interaction to DOCK180 and is critical in Rac signaling Mol. Biol. Cell 2008 19 4837 4851 18768751 PMC2575150
  29. [31]Hanawa-Suetsugu K Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms Proc. Natl Acad. Sci. USA 2012 109 3305 3310 22331897 PMC3295310
  30. [32]Guo X Chen SY Dedicator of cytokinesis 2 in cell signaling regulation and disease development J. Cell. Physiol. 2017 232 1931 1940 27504608
  31. [34]Nishikimi A Sequential regulation of DOCK2 dynamics by two phospholipids during neutrophil chemotaxis Science 2009 324 384 387 19325080 PMC3761877
  32. [35]Katoh H Negishi M RhoG activates Rac1 by direct interaction with the Dock180-binding protein Elmo Nature 2003 424 461 464 12879077
  33. [36]Patel M An evolutionarily conserved autoinhibitory molecular switch in ELMO proteins regulates Rac signaling Curr. Biol. 2010 20 2021 2027 21035343 PMC4640902
  34. [37]Patel M Chiang TC Tran V Lee FJ Cote JF The Arf family GTPase Arl4A complexes with ELMO proteins to promote actin cytoskeleton remodeling and reveals a versatile Ras-binding domain in the ELMO proteins family J. Biol. Chem. 2011 286 38969 38979 21930703 PMC3234722
  35. [38]Park D BAI1 is an engulfment receptor for apoptotic cells upstream of the ELMO/Dock180/Rac module Nature 2007 450 430 434 17960134
  36. [39]Hamoud N Tran V Croteau LP Kania A Cote JF G-protein coupled receptor BAI3 promotes myoblast fusion in vertebrates Proc. Natl Acad. Sci. USA 2014 111 3745 3750 24567399 PMC3956190
  37. [40]Hochreiter-Hufford AE Phosphatidylserine receptor BAI1 and apoptotic cells as new promoters of myoblast fusion Nature 2013 497 263 267 23615608 PMC3773542
  38. [41]Hamoud N Spatiotemporal regulation of the GPCR activity of BAI3 by C1qL4 and Stabilin-2 controls myoblast fusion Nat. Commun. 2018 9 4470 30367035 PMC6203814
  39. [42]Weng Z Structure of BAI1/ELMO2 complex reveals an action mechanism of adhesion GPCRs via ELMO family scaffolds Nat. Commun. 2019 10 51 30604775 PMC6318265
  40. [43]Kulkarni K Yang J Zhang Z Barford D Multiple factors confer specific Cdc42 and Rac protein activation by dedicator of cytokinesis (DOCK) nucleotide exchange factors J. Biol. Chem. 2011 286 25341 25351 21613211 PMC3137105
  41. [44]Yang J Zhang Z Roe SM Marshall CJ Barford D Activation of Rho GTPases by DOCK exchange factors is mediated by a nucleotide sensor Science 2009 325 1398 1402 19745154
  42. [45]Holm L Kaariainen S Rosenstrom P Schenkel A Searching protein structure databases with DaliLite v.3 Bioinforma. (Oxf., Engl.) 2008 24 2780 2781 PMC2639270 18818215
  43. [46]Jeong H Mechanistic insight into the nucleus-vacuole junction based on the Vac8p-Nvj1p crystal structure Proc. Natl Acad. Sci. USA 2017 114 E4539 E4548 28533415 PMC5468681
  44. [47]Fleishman SJ RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite PloS ONE 2011 6 e20161 21731610 PMC3123292
  45. [48]Helfmann S The crystal structure of the C(2)A domain of otoferlin reveals an unconventional top loop region J. Mol. Biol. 2011 406 479 490 21216247
  46. [49]Lu M A Steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs Curr. Biol. 2005 15 371 377 15723800
  47. [50]Grimsley CM Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration J. Biol. Chem. 2004 279 6087 6097 14638695
  48. [51]Lu M Ravichandran KS Dock180-ELMO cooperation in Rac activation Methods Enzymol. 2006 406 388 402 16472672
  49. [52]Jarzynka MJ ELMO1 and Dock180, a bipartite Rac1 guanine nucleotide exchange factor, promote human glioma cell invasion Cancer Res 2007 67 7203 7211 17671188 PMC2867339
  50. [53]Lu M PH domain of ELMO functions in trans to regulate Rac activation via Dock180 Nat. Struct. Mol. Biol. 2004 11 756 762 15247908
  51. [54]Mott HR Owen D Structures of Ras superfamily effector complexes: What have we learnt in two decades? Crit. Rev. Biochem Mol. Biol. 2015 50 85 133 25830673
  52. [55]Stieglitz B Novel type of Ras effector interaction established between tumour suppressor NORE1A and Ras switch II EMBO J. 2008 27 1995 2005 18596699 PMC2486280
  53. [56]Smith MJ Evolution of AF6-RAS association and its implications in mixed-lineage leukemia Nat. Commun. 2017 8 1099 29062045 PMC5653649
  54. [57]Abu-Thuraia A Axl phosphorylates Elmo scaffold proteins to promote Rac activation and cell invasion Mol. Cell Biol. 2015 35 76 87 25332238 PMC4295393
  55. [58]Feng H Activation of Rac1 by Src-dependent phosphorylation of Dock180(Y1811) mediates PDGFRalpha-stimulated glioma tumorigenesis in mice and humans J. Clin. Investig. 2011 121 4670 4684 22080864 PMC3223070
  56. [59]Laurin M Rac-specific guanine nucleotide exchange factor DOCK1 is a critical regulator of HER2-mediated breast cancer metastasis Proc. Natl Acad. Sci. USA 2013 110 7434 7439 23592719 PMC3645577
  57. [60]Pacold ME Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase gamma Cell 2000 103 931 943 11136978
  58. [61]Sun Y ClipR-59 interacts with Elmo2 and modulates myoblast fusion J. Biol. Chem. 2015 290 6130 6140 25572395 PMC4358253
  59. [62]Zhang Z Yang J Barford D Recombinant expression and reconstitution of multiprotein complexes by the USER cloning method in the insect cell-baculovirus expression system Methods 2016 95 13 25 26454197
  60. [63]Bitinaite J USER friendly DNA engineering and cloning method by uracil excision Nucleic Acids Res 2007 35 1992 2002 17341463 PMC1874603
  61. [64]Zheng SQ MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Nat. Methods 2017 14 331 332 28250466 PMC5494038
  62. [65]Zhang K Gctf: real-time CTF determination and correction J. Struct. Biol. 2016 193 1 12 26592709 PMC4711343
  63. [66]Fernandez-Leiro R Scheres SHW A pipeline approach to single-particle processing in RELION. Acta crystallographica. Section D Struct. Biol. 2017 73 496 502 PMC5458491 28580911
  64. [67]Nakane, T., Kimanius, D., Lindahl, E. & Scheres, S. H. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. eLife7, 10.7554/eLife.36861 (2018). PMC6005684 29856314 · DOI
  65. [68]Scheres SH RELION: implementation of a Bayesian approach to cryo-EM structure determination J. Struct. Biol. 2012 180 519 530 23000701 PMC3690530
  66. [69]Scheres SH Semi-automated selection of cryo-EM particles in RELION-1.3 J. Struct. Biol. 2015 189 114 122 25486611 PMC4318617
  67. [70]Bai, X. C., Rajendra, E., Yang, G., Shi, Y. & Scheres, S. H. Sampling the conformational space of the catalytic subunit of human gamma-secretase. eLife4, 10.7554/eLife.11182 (2015). PMC4718806 26623517 · DOI
  68. [71]Yang Z UCSF Chimera, MODELLER, and IMP: an integrated modeling system J. Struct. Biol. 2012 179 269 278 21963794 PMC3410985
  69. [72]Emsley P Lohkamp B Scott WG Cowtan K Features and development of Coot Acta Crystallogr D. Biol. Crystallogr 2010 66 486 501 20383002 PMC2852313
  70. [74]Roy A Kucukural A Zhang Y I-TASSER: a unified platform for automated protein structure and function prediction Nat. Protoc. 2010 5 725 738 20360767 PMC2849174
  71. [75]Adams PD PHENIX: a comprehensive python-based system for macromolecular structure solution Acta Crystallogr D. Biol. Crystallogr 2010 66 213 221 20124702 PMC2815670

Cited by

Sorted by citations

Authors
Chang, L., Yang, J., Jo, C. H., Boland, A., Zhang, Z., McLaughlin, S. H., Abu-Thuraia, A., Killoran, R. C., Smith, M. J., Côté, J.-F., & Barford, D.
Affiliations
  • MRC Laboratory of Molecular Biology (GB)
  • Institute for Research in Immunology and Cancer (CA)
  • University of Geneva (CH)
  • Montreal Clinical Research Institute (CA)
Corresponding author
Barford, David
Venue
Nature Communications
Published
2020-07-10
Volume
11
Issue
1
Pages
3464-3464
ISSN
2041-1723 (ISSN-L)
OpenAlex
W3041891313
Cited by
59
References
4
Citations by year
2026: 4 · 2025: 7 · 2024: 11 · 2023: 9 · 2022: 9 · 2021: 16 · 2020: 3
FWCI
3.00
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Archive ouverte UNIGE (University of Geneva) (submittedVersion, other-oa)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo (cc-by)
  • Apollo
Funders
  • Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre
  • Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada
  • RCUK | Medical Research Council (MC_UP_1201/6)
  • Cancer Research UK (C576/A14109)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
Keywords
DOCK2, ELMO1, guanine nucleotide exchange factor, Rac1, Rho GTPases, autoinhibition, Ras-binding domain, RhoG, actin dynamics, protein complex structure, phosphorylation, conformational change
MeSH terms
Calorimetry, HeLa Cells, Humans, Kinetics, Microscopy, Electron, Phosphorylation, Immunoblotting, Guanine Nucleotide Exchange Factors, GTPase-Activating Proteins, rho GTP-Binding Proteins, rac1 GTP-Binding Protein, Adaptor Proteins, Signal Transducing, HEK293 Cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review