CoChat
Sign Up
Cited by 82Protein Kinase Regulation and GTPase SignalingCellular Mechanics and InteractionsProtein Structure and Dynamics

Structures reveal a key mechanism of WAVE regulatory complex activation by Rac1 GTPase

Open access
Ding, Bojian, Yang, Sheng, Schaks, Matthias, Liu, Yijun, Brown, Abbigale J., Rottner, Klemens, Chowdhury, Saikat, Chen, Baoyu·2022·Nature Communications
DOI 10.1038/s41467-022-33174-3PMC PMC9481577

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

The Rho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites—the A and D sites. Precisely how Rac1 binds and how the binding triggers WRC activation remain unknown. Here we report WRC structures by itself, and when bound to single or double Rac1 molecules, at ~3 Å resolutions by cryogenic-electron microscopy. The structures reveal that Rac1 binds to the two sites by distinct mechanisms, and binding to the A site, but not the D site, drives WRC activation. Activation involves a series of unique conformational changes leading to the release of sequestered WCA (WH2-central-acidic) polypeptide, which stimulates the Arp2/3 complex to polymerize actin. Together with biochemical and cellular analyses, the structures provide a novel mechanistic understanding of how the Rac1-WRC-Arp2/3-actin signaling axis is regulated in diverse biological processes and diseases.

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/s41467-022-33174-3

Cites

2 of 2 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?

  • Structural studies of the WAVE complex in vitro have used a recombinant WAVE complex containing mini-WAVE, which lacks the proline-rich region due to the disordered nature of this region and difficulty in crystallization.

    “Structural studies of the WAVE complex in vitro have used a recombinant WAVE complex containing mini-WAVE21,28,30,172, which lacks the proline-rich region due to the disordered nature of this region and difficulty in crystallization21.”

    From The WAVE complex in developmental and adulthood brain disorders (2025) · cites this paper as [30]

    The Results section (‘Structural solutions to understand Rac1 binding to WRC’; page unavailable) says earlier crystal structures used a minimal WRC lacking WAVE1 residues 187–230, and that this region appears disordered in the paper’s cryo-EM reconstructions. It does not identify that deletion as the entire proline-rich region or say that difficulty in crystallization was the reason for omitting it. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Rac1 binds to two sites on CYFIP in the WAVE complex, leading to WAVE activation.

    “Rac1 binds to two sites on CYFIP in the WAVE complex, leading to WAVE activation28,30–32.”

    From The WAVE complex in developmental and adulthood brain disorders (2025) · cites this paper as [30]

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: 45

  1. [1]Campellone KG Welch MD A nucleator arms race: cellular control of actin assembly Nat. Rev. Mol. Cell Biol. 2010 11 237 251 10.1038/nrm2867 20237478 PMC2929822 · DOI
  2. [2]Alekhina O Burstein E Billadeau DD Cellular functions of WASP family proteins at a glance J. Cell Sci. 2017 130 2235 2241 28646090 PMC5536917
  3. [3]Kramer DA Piper HK Chen B WASP family proteins: molecular mechanisms and implications in human disease Eur. J. Cell Biol. 2022 101 151244 10.1016/j.ejcb.2022.151244 35667337 PMC9357188 · DOI · Paper page
  4. [4]Kim AS Kakalis LT Abdul-Manan N Liu GA Rosen MK Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein Nature 2000 404 151 158 10.1038/35004513 10724160 · DOI
  5. [5]Takenawa T Suetsugu S The WASP-WAVE protein network: connecting the membrane to the cytoskeleton Nat. Rev. Mol. Cell Biol. 2007 8 37 48 10.1038/nrm2069 17183359 · DOI · Paper page
  6. [6]Eden S Rohatgi R Podtelejnikov AV Mann M Kirschner MW Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck Nature 2002 418 790 793 10.1038/nature00859 12181570 · DOI · Paper page
  7. [7]Ismail AM Padrick SB Chen B Umetani J Rosen MK The WAVE regulatory complex is inhibited Nat. Struct. Mol. Biol. 2009 16 561 563 10.1038/nsmb.1587 19363480 PMC2716658 · DOI
  8. [8]Derivery E Lombard B Loew D Gautreau A The wave complex is intrinsically inactive Cell Motil. Cytoskelet. 2009 66 777 790 10.1002/cm.20342 19206172 · DOI
  9. [9]Chen Z Structure and control of the actin regulatory WAVE complex Nature 2010 468 533 538 10.1038/nature09623 21107423 PMC3085272 · DOI · Paper page
  10. [10]Jia D WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes Proc. Natl Acad. Sci. USA 2010 107 10442 10447 10.1073/pnas.0913293107 20498093 PMC2890800 · DOI
  11. [11]Padrick SB Hierarchical regulation of WASP/WAVE proteins Mol. Cell 2008 32 426 438 10.1016/j.molcel.2008.10.012 18995840 PMC2680354 · DOI
  12. [12]Koronakis V WAVE regulatory complex activation by cooperating GTPases Arf and Rac1 Proc. Natl Acad. Sci. USA 2011 108 14449 14454 10.1073/pnas.1107666108 21844371 PMC3167530 · DOI · Paper page
  13. [13]Chen B The WAVE regulatory complex links diverse receptors to the actin cytoskeleton Cell 2014 156 195 207 10.1016/j.cell.2013.11.048 24439376 PMC4059610 · DOI · Paper page
  14. [14]Chen B Rac1 GTPase activates the WAVE regulatory complex through two distinct binding sites Elife 2017 6 e29795 10.7554/eLife.29795 28949297 PMC5614565 · DOI · Paper page
  15. [15]Lebensohn AM Kirschner MW Activation of the WAVE complex by coincident signals controls actin assembly Mol. Cell 2009 36 512 10.1016/j.molcel.2009.10.024 19917258 PMC2818508 · DOI · Paper page
  16. [16]Hao YH Regulation of WASH-dependent actin polymerization and protein trafficking by ubiquitination Cell 2013 152 1051 1064 10.1016/j.cell.2013.01.051 23452853 PMC3640276 · DOI
  17. [17]Prehoda KE Scott JA Mullins RD Lim WA Integration of multiple signals through cooperative regulation of the N- WASP-Arp2/3 complex Science 2000 290 801 806 10.1126/science.290.5492.801 11052943 · DOI
  18. [18]Abdul-Manan, N. et al. Structure of Cdc42 in complex with the GTPase-binding domain of the ‘Wiskott-Aldrich syndrome’ protein. Nature10.1038/20726 (1999). 10360578
  19. [19]Rottner K Stradal TEB Chen B WAVE regulatory complex Curr. Biol. 2021 31 R512 R517 10.1016/j.cub.2021.01.086 34033782 PMC8882368 · DOI · Paper page
  20. [20]Chen XJ Ena/VASP proteins cooperate with the WAVE complex to regulate the actin cytoskeleton Dev. Cell 2014 30 569 584 10.1016/j.devcel.2014.08.001 25203209 PMC4165403 · DOI
  21. [21]Schaks, M. et al. Distinct interaction sites of Rac GTPase with WAVE regulatory complex have non-redundant functions in vivo. Curr. Biol. 28, 674–3684.e6 (2018). PMC6264382 30393033
  22. [22]Krauthammer M Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma Nat. Genet 2012 44 1006 1014 10.1038/ng.2359 22842228 PMC3432702 · DOI · Paper page
  23. [24]Kaplan, E., Stone, R., Hume, P. J., Greene, N. P. & Koronakis, V. Structure of CYRI-B (FAM49B), a key regulator of cellular actin assembly. Acta Crystallogr. Sect. D Struct. Biol. 76, 1015–1024 (2020). PMC7543656 33021503
  24. [25]Fort, L. et al. Fam49/CYRI interacts with Rac1 and locally suppresses protrusions. Nat. Cell Biol. 20, 1159–1171 (2018). PMC6863750 30250061
  25. [26]Yelland, T. et al. Structural basis of CYRI-B direct competition with Scar/WAVE complex for Rac1. Structure29, 226–237.e4 (2021). PMC7955166 33217330
  26. [27]Zweier M Spatially clustering de novo variants in CYFIP2, encoding the cytoplasmic FMRP interacting protein 2, cause intellectual disability and seizures Eur. J. Hum. Genet. 2019 27 747 759 10.1038/s41431-018-0331-z 30664714 PMC6461771 · DOI · Paper page
  27. [28]Schaks, M., Reinke, M., Witke, W. & Rottner, K. Molecular dissection of neurodevelopmental disorder-causing mutations in CYFIP2. Cells9, 1355 (2020). PMC7348743 32486060
  28. [29]Nakashima M De novo hotspot variants in CYFIP2 cause early-onset epileptic encephalopathy Ann. Neurol. 2018 83 794 806 10.1002/ana.25208 29534297 · DOI · Paper page
  29. [30]Begemann, A. et al. New insights into the clinical and molecular spectrum of the novel CYFIP2-related neurodevelopmental disorder and impairment of the WRC-mediated actin dynamics. Genet. Med. 23, 543–554 (2021). PMC7935717 33149277
  30. [31]Leng Y Abelson-interactor-1 promotes WAVE2 membrane translocation and Abelson-mediated tyrosine phosphory lation required for WAVE2 activation Proc. Natl Acad. Sci. USA 2005 102 1098 1103 10.1073/pnas.0409120102 15657136 PMC545868 · DOI · Paper page
  31. [32]Stuart, J. R., Gonzalez, F. H., Kawai, H. & Yuan, Z. M. c-Abl interacts with the WAVE2 signaling complex to induce membrane ruffling and cell spreading. J. Biol. Chem. 281, 31290–31297 (2006). 16899465
  32. [33]Sossey-Alaoui, K., Li, X. & Cowell, J. K. c-Abl-mediated phosphorylation of WAVE3 is required for lamellipodia formation and cell migration. J. Biol. Chem. 282, 26257–26265 (2007). 17623672
  33. [34]Torres E Rosen MK Contingent phosphorylation/dephosphorylation provides a mechanism of molecular memory in WASP Mol. Cell 2003 11 1215 1227 10.1016/S1097-2765(03)00139-4 12769846 · DOI
  34. [35]Chen B Padrick SB Henry L Rosen MK Biochemical reconstitution of the WAVE regulatory complex Methods Enzymol. 2014 540 55 72 10.1016/B978-0-12-397924-7.00004-2 24630101 PMC4110903 · DOI
  35. [36]Zheng, S. Q. et al. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods. 14, 331–332 (2017). PMC5494038 28250466
  36. [37]Scheres SH RELION: implementation of a Bayesian approach to cryo-EM structure determination J. Struct. Biol. 2012 180 519 530 10.1016/j.jsb.2012.09.006 23000701 PMC3690530 · DOI · Paper page
  37. [38]Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016). PMC4711343 26592709
  38. [39]Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. CryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods10.1038/nmeth.4169 (2017). 28165473
  39. [40]Pettersen EF UCSF Chimera—a visualization system for exploratory research and analysis J. Comput Chem. 2004 25 1605 1612 10.1002/jcc.20084 15264254 · DOI
  40. [41]Kidmose, R. T. et al. Namdinator—Automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps. IUCrJ6, 526–531 (2019). PMC6608625 31316797
  41. [43]Chen, V. B. et al. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 12–21 (2010). PMC2803126 20057044
  42. [44]Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 10.1093/nar/gkl971 (2007). PMC1669775 17142228 · DOI
  43. [45]Jurrus, E. et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27, 112–128. (2018). PMC5734301 28836357
  44. [46]Pettersen EF UCSF ChimeraX: Structure visualization for researchers, educators, and developers Protein Sci. 2021 30 70 82 10.1002/pro.3943 32881101 PMC7737788 · DOI
  45. [47]Steffen, A. et al. Sra-1 and Nap1 link Rac to actin assembly driving lamellipodia formation. EMBO J. 23, 749–759 (2004). PMC380996 14765121

Cited by

Sorted by citations

Authors
Ding, B., Yang, S., Schaks, M., Liu, Y., Brown, A. J., Rottner, K., Chowdhury, S., & Chen, B.
Affiliations
  • Stony Brook University (US)
  • Iowa State University (US)
  • Helmholtz Centre for Infection Research (DE)
  • Centre for Cellular and Molecular Biology (IN)
Corresponding author
  • Chowdhury, Saikat
  • Chen, Baoyu
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2022-09-16
Volume
13
Issue
1
Pages
5444-5444
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-022-33174-3
PMC
PMC9481577
OpenAlex
W4296041547
Cited by
82
References
2
Citations by year
2026: 20 · 2025: 25 · 2024: 19 · 2023: 14 · 2022: 3 · 2020: 1
FWCI
4.97
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Iowa State University Digital Repository (Iowa State University) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Deutsche Forschungsgemeinschaft (RO2414/8-1)
  • Stony Brook University start-up funds
  • U.S. Department of Health & Human Services | National Institutes of Health (R35-GM128786)
  • start-up funds from the Iowa State University and the Roy J. Carver Charitable Trust
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 Mechanics and Interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
WAVE regulatory complex, Rac1, Rho GTPases, Arp2/3 complex, actin polymerization, WH2 domain, protein complex structure, protein-protein binding, conformational change, actin cytoskeleton regulation
MeSH terms
Actins, Cytoplasm, rac1 GTP-Binding Protein, Wiskott-Aldrich Syndrome Protein Family, Actin-Related Protein 2-3 Complex

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