+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26733 | |||||||||
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Title | Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex | |||||||||
Map data | WRC230VCA-Rac1 complex sharpened map | |||||||||
Sample |
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Function / homology | Function and homology information peripheral region of growth cone / negative regulation of synaptic vesicle recycling / intracellular protein-containing complex / 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 ...peripheral region of growth cone / negative regulation of synaptic vesicle recycling / intracellular protein-containing complex / 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 / regulation of respiratory burst / central region of growth cone / modification of postsynaptic actin cytoskeleton / negative regulation of interleukin-23 production / dendrite extension / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of translation at postsynapse, modulating synaptic transmission / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / filopodium tip / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / : / regulation of modification of postsynaptic actin cytoskeleton / cortical cytoskeleton organization / respiratory burst / regulation of actin filament polymerization / hepatocyte growth factor receptor signaling pathway / RNA 7-methylguanosine cap binding / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / axon extension / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / positive regulation of ruffle assembly / positive regulation of dendrite development / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / protein kinase A binding / lamellipodium assembly / regulation of myelination / cortical actin cytoskeleton organization / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / positive regulation of actin filament polymerization / NRAGE signals death through JNK / Rac protein signal transduction / protein kinase A regulatory subunit binding / filamentous actin / RHO GTPases activate PAKs / dendritic growth cone / positive regulation of focal adhesion assembly / lamellipodium membrane / semaphorin-plexin signaling pathway / excitatory synapse / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / positive regulation of axon extension / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / axonal growth cone / response to electrical stimulus Similarity search - Function | |||||||||
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
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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 ...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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26733.map.gz | 12.6 MB | EMDB map data format | |
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Header (meta data) | emd-26733-v30.xml emd-26733.xml | 30.6 KB 30.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26733_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_26733.png | 115.7 KB | ||
Masks | emd_26733_msk_1.map | 64 MB | Mask map | |
Others | emd_26733_additional_1.map.gz emd_26733_half_map_1.map.gz emd_26733_half_map_2.map.gz | 9.2 MB 59 MB 59 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26733 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26733 | HTTPS FTP |
-Related structure data
Related structure data | 7usdMC 7uscC 7useC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26733.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | WRC230VCA-Rac1 complex sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8757 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26733_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: WRC230VCA-Rac1 complex masked unsharpened map
File | emd_26733_additional_1.map | ||||||||||||
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Annotation | WRC230VCA-Rac1 complex masked unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: WRC230VCA-Rac1 complex unmasked unfiltered unsharpened first half map
File | emd_26733_half_map_1.map | ||||||||||||
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Annotation | WRC230VCA-Rac1 complex unmasked unfiltered unsharpened first half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: WRC230VCA-Rac1 complex unmasked unfiltered unsharpened second half map...
File | emd_26733_half_map_2.map | ||||||||||||
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Annotation | WRC230VCA-Rac1 complex unmasked unfiltered unsharpened second half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : WAVE regulatory complex with Rac1 bound to D-site
Entire | Name: WAVE regulatory complex with Rac1 bound to D-site |
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Components |
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-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 |
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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 ...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 |
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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 ...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 ...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 |
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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 ...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 ...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 |
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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 ...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 ...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 |
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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 ...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 |
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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 |
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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 |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #8: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.41 mg/mL |
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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 |
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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/Å2 Details: Each micrograph was acquired as dose-fractionated movies consisting of 62 frames per movie. |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |