EMDB-26733: Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex

Basic information

Entry

Database: EMDB / ID: EMD-26733

• Title: Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex
• Map data: WRC230VCA-Rac1 complex sharpened map

Sample

• Complex: WAVE regulatory complex with Rac1 bound to D-site
  • Protein or peptide: Cytoplasmic FMR1-interacting protein 1
  • Protein or peptide: Nck-associated protein 1
  • Protein or peptide: Wiskott-Aldrich syndrome protein family member 1
  • Protein or peptide: Protein BRICK1
  • Protein or peptide: Abl interactor 2
  • Protein or peptide: Ras-related C3 botulinum toxin substrate 1
• Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
• Ligand: MAGNESIUM ION

Function / homology

Function:

dendritic transport of mitochondrion / peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / central region of growth cone / dendrite extension / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of synaptic structure / regulation of actin polymerization or depolymerization / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / regulation of modification of postsynaptic actin cytoskeleton / Activated NTRK2 signals through CDK5 / regulation of translation at postsynapse, modulating synaptic transmission / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Rho GDP-dissociation inhibitor binding / Inactivation of CDC42 and RAC1 / filopodium tip / regulation of actin filament polymerization / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / cell projection assembly / RHO GTPases activate CIT / RNA 7-methylguanosine cap binding / RHO GTPases activate KTN1 / cortical cytoskeleton organization / ruffle organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / actin polymerization or depolymerization / regulation of nitric oxide biosynthetic process / Azathioprine ADME / regulation of stress fiber assembly / negative regulation of fibroblast migration / sphingosine-1-phosphate receptor signaling pathway / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of lamellipodium assembly / Nef and signal transduction / motor neuron axon guidance / Sema4D mediated inhibition of cell attachment and migration / Activation of RAC1 / positive regulation of ruffle assembly / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Ephrin signaling / positive regulation of dendrite development / mitochondrion morphogenesis / translation regulator activity / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / regulation of myelination / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / cortical actin cytoskeleton organization / regulation of cell size / Rac protein signal transduction / DSCAM interactions / protein kinase A binding / positive regulation of lamellipodium assembly / establishment or maintenance of cell polarity / small GTPase mediated signal transduction / RHO GTPases activate PAKs / filamentous actin / protein kinase A regulatory subunit binding / ficolin-1-rich granule membrane / positive regulation of axon extension / positive regulation of actin filament polymerization / dendritic growth cone / positive regulation of focal adhesion assembly / lamellipodium membrane / excitatory synapse / RHOG GTPase cycle / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases activate IQGAPs / axon extension / anatomical structure morphogenesis / cellular response to brain-derived neurotrophic factor stimulus / RAC3 GTPase cycle / RAC2 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases

Domain/homology:

Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / ABL interactor 2 / CYRIA/CYRIB, Rac1 binding domain / Abl-interactor, homeo-domain homologous domain / SCAR/WAVE family / ABI family / CYRIA/CYRIB Rac1 binding domain / Abl-interactor HHR / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / small GTPase Rho family profile. / Small GTPase Rho / Variant SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase

Component:

Abl interactor 2 / Ras-related C3 botulinum toxin substrate 1 / Cytoplasmic FMR1-interacting protein 1 / Protein BRICK1 / Actin-binding protein WASF1 / Nck-associated protein 1

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.0 Å
• Authors: Ding B / Yang S / Chen B / Chowdhury S

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		United States

• Citation: Journal: Nat Commun / Year: 2022; Title: Structures reveal a key mechanism of WAVE regulatory complex activation by Rac1 GTPase.; Authors: Bojian Ding / Sheng Yang / Matthias Schaks / Yijun Liu / Abbigale J Brown / Klemens Rottner / Saikat Chowdhury / Baoyu Chen / ; 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.

History

Deposition	Apr 25, 2022	-
Header (metadata) release	Sep 21, 2022	-
Map release	Sep 21, 2022	-
Update	Nov 9, 2022	-
Current status	Nov 9, 2022	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_26733.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: WRC230VCA-Rac1 complex sharpened map
• Voxel size: X=Y=Z: 0.8757 Å

Density

Contour Level	By AUTHOR: 0.023
Minimum - Maximum	-0.056113258 - 0.20268014
Average (Standard dev.)	0.00080763036 (±0.0066834274)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 256 256 256 Spacing 256 256 256
Cell	A=B=C: 224.1792 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_26733_msk_1.map

Additional map: WRC230VCA-Rac1 complex masked unsharpened map

• File: emd_26733_additional_1.map
• Annotation: WRC230VCA-Rac1 complex masked unsharpened map

Half map: WRC230VCA-Rac1 complex unmasked unfiltered unsharpened first half map

• File: emd_26733_half_map_1.map
• Annotation: WRC230VCA-Rac1 complex unmasked unfiltered unsharpened first half map

Half map: WRC230VCA-Rac1 complex unmasked unfiltered unsharpened second half map...

• File: emd_26733_half_map_2.map
• Annotation: WRC230VCA-Rac1 complex unmasked unfiltered unsharpened second half map

Sample components

Entire : WAVE regulatory complex with Rac1 bound to D-site

• Entire: Name: WAVE regulatory complex with Rac1 bound to D-site

Components

• Complex: WAVE regulatory complex with Rac1 bound to D-site
  • Protein or peptide: Cytoplasmic FMR1-interacting protein 1
  • Protein or peptide: Nck-associated protein 1
  • Protein or peptide: Wiskott-Aldrich syndrome protein family member 1
  • Protein or peptide: Protein BRICK1
  • Protein or peptide: Abl interactor 2
  • Protein or peptide: Ras-related C3 botulinum toxin substrate 1
• Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
• Ligand: MAGNESIUM ION

Supramolecule #1: WAVE regulatory complex with Rac1 bound to D-site

• Supramolecule: Name: WAVE regulatory complex with Rac1 bound to D-site / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 360 KDa

Macromolecule #1: Cytoplasmic FMR1-interacting protein 1

• Macromolecule: Name: Cytoplasmic FMR1-interacting protein 1 / type: protein_or_peptide / ID: 1 ; Details: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts.; Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 145.36375 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MAAQVTLEDA LSNVDLLEEL PLPDQQPCIE PPPSSLLYQP NFNTNFEDRN AFVTGIARYI EQATVHSSMN EMLEEGQEYA VMLYTWRSC SRAIPQVKCN EQPNRVEIYE KTVEVLEPEV TKLMNFMYFQ RNAIERFCGE VRRLCHAERR KDFVSEAYLI T LGKFINMF AVLDELKNMK CSVKNDHSAY KRAAQFLRKM ADPQSIQESQ NLSMFLANHN KITQSLQQQL EVISGYEELL AD IVNLCVD YYENRMYLTP SEKHMLLKVM GFGLYLMDGS VSNIYKLDAK KRINLSKIDK YFKQLQVVPL FGDMQIELAR YIK TSAHYE ENKSRWTCTS SGSSPQYNIC EQMIQIREDH MRFISELARY SNSEVVTGSG RQEAQKTDAE YRKLFDLALQ GLQL LSQWS AHVMEVYSWK LVHPTDKYSN KDCPDSAEEY ERATRYNYTS EEKFALVEVI AMIKGLQVLM GRMESVFNHA IRHTV YAAL QDFSQVTLRE PLRQAIKKKK NVIQSVLQAI RKTVCDWETG HEPFNDPALR GEKDPKSGFD IKVPRRAVGP SSTQLY MVR TMLESLIADK SGSKKTLRSS LEGPTILDIE KFHRESFFYT HLINFSETLQ QCCDLSQLWF REFFLELTMG RRIQFPI EM SMPWILTDHI LETKEASMME YVLYSLDLYN DSAHYALTRF NKQFLYDEIE AEVNLCFDQF VYKLADQIFA YYKVMAGS L LLDKRLRSEC KNQGATIHLP PSNRYETLLK QRHVQLLGRS IDLNRLITQR VSAAMYKSLE LAIGRFESED LTSIVELDG LLEINRMTHK LLSRYLTLDG FDAMFREANH NVSAPYGRIT LHVFWELNYD FLPNYCYNGS TNRFVRTVLP FSQEFQRDKQ PNAQPQYLH GSKALNLAYS SIYGSYRNFV GPPHFQVICR LLGYQGIAVV MEELLKVVKS LLQGTILQYV KTLMEVMPKI C RLPRHEYG SPGILEFFHH QLKDIVEYAE LKTVCFQNLR EVGNAILFCL LIEQSLSLEE VCDLLHAAPF QNILPRVHVK EG ERLDAKM KRLESKYAPL HLVPLIERLG TPQQIAIARE GDLLTKERLC CGLSMFEVIL TRIRSFLDDP IWRGPLPSNG VMH VDECVE FHRLWSAMQF VYCIPVGTHE FTVEQCFGDG LHWAGCMIIV LLGQQRRFAV LDFCYHLLKV QKHDGKDEII KNVP LKKMV ERIRKFQILN DEIITILDKY LKSGDGEGTP VEHVRCFQPP IHQSLASS

Macromolecule #2: Nck-associated protein 1

• Macromolecule: Name: Nck-associated protein 1 / type: protein_or_peptide / ID: 2 ; Details: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts.; Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 128.940727 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MSRSVLQPSQ QKLAEKLTIL NDRGVGMLTR LYNIKKACGD PKAKPSYLID KNLESAVKFI VRKFPAVETR NNNQQLAQLQ KEKSEILKN LALYYFTFVD VMEFKDHVCE LLNTIDVCQV FFDITVNFDL TKNYLDLIIT YTTLMILLSR IEERKAIIGL Y NYAHEMTH GASDREYPRL GQMIVDYENP LKKMMEEFVP HSKSLSDALI SLQMVYPRRN LSADQWRNAQ LLSLISAPST ML NPAQSDT MPCEYLSLDA MEKWIIFGFI LCHGILNTDA TALNLWKLAL QSSSCLSLFR DEVFHIHKAA EDLFVNIRGY NKR INDIRE CKEAAVSHAG SMHRERRKFL RSALKELATV LSDQPGLLGP KALFVFMALS FARDEIIWLL RHADNMPKKS ADDF IDKHI AELIFYMEEL RAHVRKYGPV MQRYYVQYLS GFDAVVLNEL VQNLSVCPED ESIIMSSFVN TMTSLSVKQV EDGEV FDFR GMRLDWFRLQ AYTSVSKASL GLADHRELGK MMNTIIFHTK MVDSLVEMLV ETSDLSIFCF YSRAFEKMFQ QCLELP SQS RYSIAFPLLC THFMSCTHEL CPEERHHIGD RSLSLCNMFL DEMAKQARNL ITDICTEQCT LSDQLLPKHC AKTISQA VN KKSKKQTGKK GEPEREKPGV ESMRKNRLVV TNLDKLHTAL SELCFSINYV PNMVVWEHTF TPREYLTSHL EIRFTKSI V GMTMYNQATQ EIAKPSELLT SVRAYMTVLQ SIENYVQIDI TRVFNNVLLQ QTQHLDSHGE PTITSLYTNW YLETLLRQV SNGHIAYFPA MKAFVNLPTE NELTFNAEEY SDISEMRSLS ELLGPYGMKF LSESLMWHIS SQVAELKKLV VENVDVLTQM RTSFDKPDQ MAALFKRLSS VDSVLKRMTI IGVILSFRSL AQEALRDVLS YHIPFLVSSI EDFKDHIPRE TDMKVAMNVY E LSSAAGLP CEIDPALVVA LSSQKSENIS PEEEYKIACL LMVFVAVSLP TLASNVMSQY SPAIEGHCNN IHCLAKAINQ IA AALFTIH KGSIEDRLKE FLALASSSLL KIGQETDKTT TRNRESVYLL LDMIVQESPF LTMDLLESCF PYVLLRNAYH AVY KQSVTS SA

Macromolecule #3: Wiskott-Aldrich syndrome protein family member 1

• Macromolecule: Name: Wiskott-Aldrich syndrome protein family member 1 / type: protein_or_peptide / ID: 3 ; Details: Residues 231-248 are inserted as a flexible linker sequence. This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts.; Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 37.009406 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MPLVKRNIDP RHLCHTALPR GIKNELECVT NISLANIIRQ LSSLSKYAED IFGELFNEAH SFSFRVNSLQ ERVDRLSVSV TQLDPKEEE LSLQDITMRK AFRSSTIQDQ QLFDRKTLPI PLQETYDVCE QPPPLNILTP YRDDGKEGLK FYTNPSYFFD L WKEKMLQD TEDKRKEKRK QKQKNLDRPH EPEKVPRAPH DRRREWQKLA QGPELAEDDA NLLHKHIEVA NGGGSGGSGG SG GSGGSGG SKRHPSTLPV ISDARSVLLE AIRKGIQLRK VEEQREQEAK HERIENDVAT ILSRRIAVEY SDSEDDSEFD EVD WLE

Macromolecule #4: Protein BRICK1

• Macromolecule: Name: Protein BRICK1 / type: protein_or_peptide / ID: 4 ; Details: This construct contains uncleaved residues "GHMGAA" in the N terminus from the construct design and purification procedure. Densities for the residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts.; Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 8.756915 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MAGQEDPVQR EIHQDWANRE YIEIITSSIK KIADFLNSFD MSCRSRLATL NEKLTALERR IEYIEARVTK GETLT

Macromolecule #5: Abl interactor 2

• Macromolecule: Name: Abl interactor 2 / type: protein_or_peptide / ID: 5 ; Details: The sequence only contains residues 1-158. Also, there are two additional uncleaved residues "GH" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts.; Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 18.041482 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MAELQMLLEE EIPGGRRALF DSYTNLERVA DYCENNYIQS ADKQRALEET KAYTTQSLAS VAYLINTLAN NVLQMLDIQA SQLRRMESS INHISQTVDI HKEKVARREI GILTTNKNTS RTHKIIAPAN LERPVRYIRK PIDYTILDDI GHGVKVSTQ

Macromolecule #6: Ras-related C3 botulinum toxin substrate 1

• Macromolecule: Name: Ras-related C3 botulinum toxin substrate 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 21.010486 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MQAIKCVVVG DGAVGKTCLL ISYTTNAFSG EYIPTVFDNY SANVMVDGKP VNLGLWDTAG LEDYDRLRPL SYPQTDVFLI CFSLVSPAS FENVRAKWYP EVRHHCPNTP IILVGTKLDL RDDKDTIEKL KEKKLTPITY PQGLAMAKEI GAVKYLECSA L TQRGLKTV FDEAIRAVLC PPPVKKRKRK

Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

• Macromolecule: Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: GTP
• Molecular weight: Theoretical: 523.18 Da

Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

Macromolecule #8: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.41 mg/mL
• Buffer: pH: 7
• Grid: Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: 30 mA
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER

Electron microscopy

• Microscope: FEI TALOS ARCTICA
• Electron beam: Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Details: Data were collected by shifting the stage to target exposure positions.
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 2512 / Average exposure time: 40.0 sec. / Average electron dose: 45.27 e/Ų; Details: Each micrograph was acquired as dose-fractionated movies consisting of 62 frames per movie.
• Experimental equipment: Model: Talos Arctica / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 1765193
• CTF correction: Software - Name: Gctf; Details: Particles were CTF-corrected during projection matching and back projection
• Initial angle assignment: Type: NOT APPLICABLE
• Final 3D classification: Number classes: 3 / Software - Name: RELION (ver. 3.1 beta) / Details: Classification without alignment
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1 beta)
• Final reconstruction: Number classes used: 1 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1 beta) / Number images used: 87810

Atomic model buiding 1

Initial model

(PDB ID:

3p8c

,

3sbd

)

• Refinement: Space: REAL / Protocol: FLEXIBLE FIT

Output model

PDB-7usd:
Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex