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- EMDB-26732: Cryo-EM structure of WAVE Regulatory Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-26732
TitleCryo-EM structure of WAVE Regulatory Complex
Map dataWRC230VCA complex sharpened map
Sample
  • Complex: WAVE regulatory complex
    • 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
Keywordsactin regulator / GTPase binding protein / cytoskeletal regulator / CELL INVASION
Function / homology
Function and homology information


peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone ...peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone / modification of postsynaptic actin cytoskeleton / dendrite extension / regulation of translation at postsynapse, modulating synaptic transmission / filopodium tip / regulation of modification of postsynaptic actin cytoskeleton / regulation of actin filament polymerization / RNA 7-methylguanosine cap binding / ruffle organization / cell projection assembly / axon extension / positive regulation of ruffle assembly / positive regulation of dendrite development / lamellipodium assembly / regulation of myelination / cortical actin cytoskeleton organization / protein kinase A binding / positive regulation of actin filament polymerization / Rac protein signal transduction / protein kinase A regulatory subunit binding / dendritic growth cone / filamentous actin / lamellipodium membrane / excitatory synapse / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / positive regulation of axon extension / response to electrical stimulus / positive regulation of lamellipodium assembly / axonal growth cone / translation repressor activity / ruffle / cellular response to brain-derived neurotrophic factor stimulus / RAC1 GTPase cycle / actin filament polymerization / receptor-mediated endocytosis / neuron projection morphogenesis / filopodium / axon guidance / actin filament organization / central nervous system development / mitochondrion organization / cell motility / FCGR3A-mediated phagocytosis / positive regulation of protein-containing complex assembly / cell morphogenesis / terminal bouton / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / cognition / cellular response to insulin stimulus / small GTPase binding / specific granule lumen / positive regulation of fibroblast proliferation / actin filament binding / cell migration / actin cytoskeleton / tertiary granule lumen / lamellipodium / regulation of translation / regulation of cell shape / actin binding / actin cytoskeleton organization / fibroblast proliferation / protein-containing complex assembly / secretory granule lumen / in utero embryonic development / mitochondrial outer membrane / postsynapse / dendritic spine / cytoskeleton / neuron projection / intracellular membrane-bounded organelle / focal adhesion / neuronal cell body / Neutrophil degranulation / synapse / protein-containing complex binding / apoptotic process / perinuclear region of cytoplasm / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain / Abl-interactor, homeo-domain homologous domain / SCAR/WAVE family / ABI family ...Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain / Abl-interactor, homeo-domain homologous domain / SCAR/WAVE family / ABI family / CYRIA/CYRIB Rac1 binding domain / Abl-interactor HHR / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Abl interactor 2 / Cytoplasmic FMR1-interacting protein 1 / Protein BRICK1 / Actin-binding protein WASF1 / Nck-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDing B / Yang S / Chen B / Chowdhury S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: 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 ...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
DepositionApr 25, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26732.png

Downloads & links

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Map

FileDownload / File: emd_26732.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWRC230VCA complex sharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 224.179 Å		0.88 Å/pix.
x 256 pix.
= 224.179 Å		0.88 Å/pix.
x 256 pix.
= 224.179 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8757 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.049646463 - 0.19777596
Average (Standard dev.)0.0010741575 (±0.0062081357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 224.1792 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26732_msk_1.map
Projections & Slices
AxesZYX

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Additional map: WRC230VCA complex masked unsharpened map

Fileemd_26732_additional_1.map
AnnotationWRC230VCA complex masked unsharpened map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: WRC230VCA complex unfiltered unmasked unsharpened first half map

Fileemd_26732_half_map_1.map
AnnotationWRC230VCA complex unfiltered unmasked unsharpened first half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: WRC230VCA complex unfiltered unmasked unsharpened second half map

Fileemd_26732_half_map_2.map
AnnotationWRC230VCA complex unfiltered unmasked unsharpened second half map
Projections & Slices
AxesZYX

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Sample components

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Entire : WAVE regulatory complex

EntireName: WAVE regulatory complex
Components
  • Complex: WAVE regulatory complex
    • 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

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Supramolecule #1: WAVE regulatory complex

SupramoleculeName: WAVE regulatory complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

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Macromolecule #1: Cytoplasmic FMR1-interacting protein 1

MacromoleculeName: 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 ...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 weightTheoretical: 145.36375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAQVTLEDA LSNVDLLEEL PLPDQQPCIE PPPSSLLYQP NFNTNFEDRN AFVTGIARYI EQATVHSSMN EMLEEGQEYA VMLYTWRSC SRAIPQVKCN EQPNRVEIYE KTVEVLEPEV TKLMNFMYFQ RNAIERFCGE VRRLCHAERR KDFVSEAYLI T LGKFINMF ...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

UniProtKB: Cytoplasmic FMR1-interacting protein 1

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Macromolecule #2: Nck-associated protein 1

MacromoleculeName: 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 ...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 weightTheoretical: 128.940727 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRSVLQPSQ QKLAEKLTIL NDRGVGMLTR LYNIKKACGD PKAKPSYLID KNLESAVKFI VRKFPAVETR NNNQQLAQLQ KEKSEILKN LALYYFTFVD VMEFKDHVCE LLNTIDVCQV FFDITVNFDL TKNYLDLIIT YTTLMILLSR IEERKAIIGL Y NYAHEMTH ...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

UniProtKB: Nck-associated protein 1

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

MacromoleculeName: 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 ...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 weightTheoretical: 37.009406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPLVKRNIDP RHLCHTALPR GIKNELECVT NISLANIIRQ LSSLSKYAED IFGELFNEAH SFSFRVNSLQ ERVDRLSVSV TQLDPKEEE LSLQDITMRK AFRSSTIQDQ QLFDRKTLPI PLQETYDVCE QPPPLNILTP YRDDGKEGLK FYTNPSYFFD L WKEKMLQD ...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

UniProtKB: Actin-binding protein WASF1, Actin-binding protein WASF1

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Macromolecule #4: Protein BRICK1

MacromoleculeName: 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 ...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 weightTheoretical: 8.756915 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGQEDPVQR EIHQDWANRE YIEIITSSIK KIADFLNSFD MSCRSRLATL NEKLTALERR IEYIEARVTK GETLT

UniProtKB: Protein BRICK1

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Macromolecule #5: Abl interactor 2

MacromoleculeName: 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 ...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 weightTheoretical: 18.041482 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAELQMLLEE EIPGGRRALF DSYTNLERVA DYCENNYIQS ADKQRALEET KAYTTQSLAS VAYLINTLAN NVLQMLDIQA SQLRRMESS INHISQTVDI HKEKVARREI GILTTNKNTS RTHKIIAPAN LERPVRYIRK PIDYTILDDI GHGVKVSTQ

UniProtKB: Abl interactor 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.41 mg/mL
BufferpH: 7
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
DetailsData were collected by shifting the stage to the target exposure positions.
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2913 / Average exposure time: 40.0 sec. / Average electron dose: 44.06 e/Å2
Details: Each micrograph was acquired as dose-fractionated movies consisting of 62 frames per movie.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2006821
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / 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: 95319
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1 beta)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1 beta) / Details: Classification without alignment
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3p8c


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7usc:
Cryo-EM structure of WAVE Regulatory Complex

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