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Basic information
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Title | Cryo-EM structure of the RhoG/DOCK5/ELMO1/Rac1 complex | ||||||||||||
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![]() | ELMO / DOCK / GEF / GTPASE / RHO / RAC / SIGNALING PROTEIN | ||||||||||||
Function / homology | ![]() negative regulation of vascular associated smooth muscle contraction / regulation of ruffle assembly / regulation of postsynapse assembly / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / podosome assembly / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis ...negative regulation of vascular associated smooth muscle contraction / regulation of ruffle assembly / regulation of postsynapse assembly / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / podosome assembly / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / guanyl-nucleotide exchange factor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / bone remodeling / myoblast fusion / ruffle organization / cell projection assembly / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / activation of GTPase activity / positive regulation of vascular associated smooth muscle cell migration / motor neuron axon guidance / PCP/CE pathway / podosome / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / regulation of lamellipodium assembly / Azathioprine ADME / anchoring junction / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / regulation of cell size / establishment or maintenance of cell polarity / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / phagocytosis, engulfment / NRAGE signals death through JNK / positive regulation of epithelial cell migration / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / RHOG GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / Signal transduction by L1 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / positive regulation of protein localization to plasma membrane / substrate adhesion-dependent cell spreading / GTPase activator activity / cell chemotaxis / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / guanyl-nucleotide exchange factor activity / actin filament organization / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.66 Å | ||||||||||||
![]() | Kukimoto-Niino M / Katsura K / Ishizuka-Katsura Y / Mishima-Tsumagari C / Yonemochi M / Inoue M / Nakagawa R / Kaushik R / Zhang KYJ / Shirouzu M | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: RhoG facilitates a conformational transition in the guanine nucleotide exchange factor complex DOCK5/ELMO1 to an open state. Authors: Mutsuko Kukimoto-Niino / Kazushige Katsura / Yoshiko Ishizuka-Katsura / Chiemi Mishima-Tsumagari / Mayumi Yonemochi / Mio Inoue / Reiko Nakagawa / Rahul Kaushik / Kam Y J Zhang / Mikako Shirouzu / ![]() Abstract: The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK- ...The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK-Rac pathway during engulfment and migration. Recent cryo-EM structures of the DOCK2/ELMO1 and DOCK2/ELMO1/Rac1 complexes have identified closed and open conformations that are key to understanding the autoinhibition mechanism. Nevertheless, the structural details of RhoG-mediated activation of the DOCK/ELMO complex remain elusive. Herein, we present cryo-EM structures of DOCK5/ELMO1 alone and in complex with RhoG and Rac1. The DOCK5/ELMO1 structure exhibits a closed conformation similar to that of DOCK2/ELMO1, suggesting a shared regulatory mechanism of the autoinhibitory state across DOCK-A/B subfamilies (DOCK1-5). Conversely, the RhoG/DOCK5/ELMO1/Rac1 complex adopts an open conformation that differs from that of the DOCK2/ELMO1/Rac1 complex, with RhoG binding to both ELMO1 and DOCK5. The alignment of the DOCK5 phosphatidylinositol (3,4,5)-trisphosphate binding site with the RhoG C-terminal lipidation site suggests simultaneous binding of RhoG and DOCK5/ELMO1 to the plasma membrane. Structural comparison of the apo and RhoG-bound states revealed that RhoG facilitates a closed-to-open state conformational change of DOCK5/ELMO1. Biochemical and surface plasmon resonance (SPR) assays confirm that RhoG enhances the Rac GEF activity of DOCK5/ELMO1 and increases its binding affinity for Rac1. Further analysis of structural variability underscored the conformational flexibility of the DOCK5/ELMO1/Rac1 complex core, potentially facilitating the proximity of the DOCK5 GEF domain to the plasma membrane. These findings elucidate the structural mechanism underlying the RhoG-induced allosteric activation and membrane binding of the DOCK/ELMO complex. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 140.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.4 KB 26.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.1 KB | Display | ![]() |
Images | ![]() | 157.1 KB | ||
Filedesc metadata | ![]() | 8.2 KB | ||
Others | ![]() ![]() ![]() | 140.2 MB 118.4 MB 118.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 934.8 KB | Display | ![]() |
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Full document | ![]() | 934.4 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8zj2MC ![]() 8jhkC ![]() 8xm7C ![]() 8zjiC ![]() 8zjjC ![]() 8zjkC ![]() 8zjlC ![]() 8zjmC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: RhoG/DOCK5/ELMO1/Rac1 complex with C2 symmetry and both RhoG-ELMO1...
File | emd_60136_additional_1.map | ||||||||||||
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Annotation | RhoG/DOCK5/ELMO1/Rac1 complex with C2 symmetry and both RhoG-ELMO1 NTDs ordered | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60136_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60136_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : RhoG/DOCK5/ELMO1/Rac1 complex
Entire | Name: RhoG/DOCK5/ELMO1/Rac1 complex |
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Components |
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-Supramolecule #1: RhoG/DOCK5/ELMO1/Rac1 complex
Supramolecule | Name: RhoG/DOCK5/ELMO1/Rac1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Dedicator of cytokinesis protein 5
Macromolecule | Name: Dedicator of cytokinesis protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 191.492125 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GGSGGSMARW IPTKRQKYGV AIYNYNASQD VELSLQIGDT VHILEMYEGW YRGYTLQNKS KKGIFPETYI HLKEATVEDL GQHETVIPG ELPLVQELTS TLREWAVIWR KLYVNNKLTL FRQLQQMTYS LIEWRSQILS GTLPKDELAE LKKKVTAKID H GNRMLGLD ...String: GGSGGSMARW IPTKRQKYGV AIYNYNASQD VELSLQIGDT VHILEMYEGW YRGYTLQNKS KKGIFPETYI HLKEATVEDL GQHETVIPG ELPLVQELTS TLREWAVIWR KLYVNNKLTL FRQLQQMTYS LIEWRSQILS GTLPKDELAE LKKKVTAKID H GNRMLGLD LVVRDDNGNI LDPDETSTIA LFKAHEVASK RIEEKIQEEK SILQNLDLRG QSIFSTIHTY GLYVNFKNFV CN IGEDAEL FMALYDPDQS TFISENYLIR WGSNGMPKEI EKLNNLQAVF TDLSSMDLIR PRVSLVCQIV RVGHMELKEG KKH TCGLRR PFGVAVMDIT DIIHGKVDDE EKQHFIPFQQ IAMETYIRQR QLIMSPLITS HVIGENEPLT SVLNKVIAAK EVNH KGQGL WVSLKLLPGD LTQVQKNFSH LVDRSTAIAR KMGFPEIILP GDVRNDIYVT LIHGEFDKGK KKTPKNVEVT MSVHD EEGK LLEKAIHPGA GYEGISEYKS VVYYQVKQPC WYETVKVSIA IEEVTRCHIR FTFRHRSSQE TRDKSERAFG VAFVKL MNP DGTTLQDGRH DLVVYKGDNK KMEDAKFYLT LPGTKMEMEE KELQASKNLV TFTPSKDSTK DSFQIATLIC STKLTQN VD LLGLLNWRSN SQNIKHNLKK LMEVDGGEIV KFLQDTLDAL FNIMMEMSDS ETYDFLVFDA LVFIISLIGD IKFQHFNP V LETYIYKHFS ATLAYVKLSK VLNFYVANAD DSSKTELLFA ALKALKYLFR FIIQSRVLYL RFYGQSKDGD EFNNSIRQL FLAFNMLMDR PLEEAVKIKG AALKYLPSII NDVKLVFDPV ELSVLFCKFI QSIPDNQLVR QKLNCMTKIV ESTLFRQSEC REVLLPLLT DQLSGQLDDN SNKPDHEASS QLLSNILEVL DRKDVGATAV HIQLIMERLL RRINRTVIGM NRQSPHIGSF V ACMIALLQ QMDDSHYSHY ISTFKTRQDI IDFLMETFIM FKDLIGKNVY AKDWMVMNMT QNRVFLRAIN QFAEVLTRFF MD QASFELQ LWNNYFHLAV AFLTHESLQL ETFSQAKRNK IVKKYGDMRK EIGFRIRDMW YNLGPHKIKF IPSMVGPILE VTL TPEVEL RKATIPIFFD MMQCEFNFSG NGNFHMFENE LITKLDQEVE GGRGDEQYKV LLEKLLLEHC RKHKYLSSSG EVFA LLVSS LLENLLDYRT IIMQDESKEN RMSCTVNVLN FYKEKKREDI YIRYLYKLRD LHRDCENYTE AAYTLLLHAE LLQWS DKPC VPHLLQRDSY YVYTQQELKE KLYQEIISYF DKGKMWEKAI KLSKELAETY ESKVFDYEGL GNLLKKRASF YENIIK AMR PQPEYFAVGY YGQGFPSFLR NKIFIYRGKE YERREDFSLR LLTQFPNAEK MTSTTPPGED IKSSPKQYMQ CFTVKPV MS LPPSYKDKPV PEQILNYYRA NEVQQFRYSR PFRKGEKDPD NEFATMWIER TTYTTAYTFP GILKWFEVKQ ISTEEISP L ENAIETMELT NERISNCVQQ HAWDRSLSVH PLSMLLSGIV DPAVMGGFSN YEKAFFTEKY LQEHPEDQEK VELLKRLIA LQMPLLTEGI RIHGEKLTEQ LKPLHERLSS CFRELKEKVE KHYGVITL UniProtKB: Dedicator of cytokinesis protein 5 |
-Macromolecule #2: Ras-related C3 botulinum toxin substrate 1
Macromolecule | Name: Ras-related C3 botulinum toxin substrate 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: small monomeric GTPase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.244258 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSSGSSGMQA IKCVVVGDGA VAKTCLLISY TTNAFPGEYI PTVFDNYSAN VMVDGKPVNL GLWDTAGQED YDRLRPLSYP QTDVFLICF SLVSPASFEN VRAKWYPEVR HHCPNTPIIL VGTKLDLRDD KDTIEKLKEK KLTPITYPQG LAMAKEIGAV K YLECSALT QRGLKTVFDE AIRAVL UniProtKB: Ras-related C3 botulinum toxin substrate 1 |
-Macromolecule #3: Engulfment and cell motility protein 1
Macromolecule | Name: Engulfment and cell motility protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 84.337719 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GGSGGSMPPP ADIVKVAIEW PGAYPKLMEI DQKKPLSAII KEVCDGWSLA NHEYFALQHA DSSNFYITEK NRNEIKNGTI LRLTTSPAQ NAQQLHERIQ SSSMDAKLEA LKDLASLSRD VTFAQEFINL DGISLLTQMV ESGTERYQKL QKIMKPCFGD M LSFTLTAF ...String: GGSGGSMPPP ADIVKVAIEW PGAYPKLMEI DQKKPLSAII KEVCDGWSLA NHEYFALQHA DSSNFYITEK NRNEIKNGTI LRLTTSPAQ NAQQLHERIQ SSSMDAKLEA LKDLASLSRD VTFAQEFINL DGISLLTQMV ESGTERYQKL QKIMKPCFGD M LSFTLTAF VELMDHGIVS WDTFSVAFIK KIASFVNKSA IDISILQRSL AILESMVLNS HDLYQKVAQE ITIGQLIPHL QG SDQEIQT YTIAVINALF LKAPDERRQE MANILAQKQL RSIILTHVIR AQRAINNEMA HQLYVLQVLT FNLLEDRMMT KMD PQDQAQ RDIIFELRRI AFDAESEPNN SSGSMEKRKS MYTRDYKKLG FINHVNPAMD FTQTPPGMLA LDNMLYFAKH HQDA YIRIV LENSSREDKH ECPFGRSSIE LTKMLCEILK VGELPSETCN DFHPMFFTHD RSFEEFFCIC IQLLNKTWKE MRATS EDFN KVMQVVKEQV MRALTTKPSS LDQFKSKLQN LSYTEILKIR QSERMNQEDF QSRPILELKE KIQPEILELI KQQRLN RLV EGTCFRKLNA RRRQDKFWYC RLSPNHKVLH YGDLEESPQG EVPHDSLQDK LPVADIKAVV TGKDCPHMKE KGALKQN KE VLELAFSILY DSNCQLNFIA PDKHEYCIWT DGLNALLGKD MMSDLTRNDL DTLLSMEIKL RLLDLENIQI PDAPPPIP K EPSNYDFVYD CN UniProtKB: Engulfment and cell motility protein 1 |
-Macromolecule #4: Rho-related GTP-binding protein RhoG
Macromolecule | Name: Rho-related GTP-binding protein RhoG / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.362359 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSSGSSGMQS IKCVVVGDGA VGKTCLLICY TTNAFPKEYI PTVFDNYSAQ SAVDGRTVNL NLWDTAGLEE YDRLRTLSYP QTNVFVICF SIASPPSYEN VRHKWHPEVC HHCPDVPILL VGTKKDLRAQ PDTLRRLKEQ GQAPITPQQG QALAKQIHAV R YLECSALQ ...String: GSSGSSGMQS IKCVVVGDGA VGKTCLLICY TTNAFPKEYI PTVFDNYSAQ SAVDGRTVNL NLWDTAGLEE YDRLRTLSYP QTNVFVICF SIASPPSYEN VRHKWHPEVC HHCPDVPILL VGTKKDLRAQ PDTLRRLKEQ GQAPITPQQG QALAKQIHAV R YLECSALQ QDGVKEVFAE AVRAVLNPTP IKRSGPSSGE NLYFQ UniProtKB: Rho-related GTP-binding protein RhoG |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 11976 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |