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Yorodumi- EMDB-13343: Structure of capping protein bound to the barbed end of a cytopla... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13343 | |||||||||
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Title | Structure of capping protein bound to the barbed end of a cytoplasmic actin filament | |||||||||
Map data | Locally filtered map with global B-factor | |||||||||
Sample |
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Function / homology | Function and homology information cytoskeletal calyx / : / Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / RHOD GTPase cycle / Gap junction degradation / Formation of annular gap junctions ...cytoskeletal calyx / : / Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / RHOD GTPase cycle / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / RHOF GTPase cycle / EPHB-mediated forward signaling / COPI-independent Golgi-to-ER retrograde traffic / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / RHO GTPases Activate Formins / F-actin capping protein complex / WASH complex / COPI-mediated anterograde transport / DNA Damage Recognition in GG-NER / negative regulation of filopodium assembly / UCH proteinases / VEGFA-VEGFR2 Pathway / structural constituent of postsynaptic actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / dense body / Clathrin-mediated endocytosis / cell projection organization / cell junction assembly / MHC class II antigen presentation / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / cortical cytoskeleton / NuA4 histone acetyltransferase complex / brush border / asymmetric synapse / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / axonogenesis / actin filament / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / Schaffer collateral - CA1 synapse / Z disc / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / actin cytoskeleton organization / dendritic spine / postsynaptic density / cytoskeleton / hydrolase activity / axon / focal adhesion / neuronal cell body / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Bovine (cattle) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Funk J / Merino F / Schacks M / Rottner K / Raunser S / Bieling P | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: A barbed end interference mechanism reveals how capping protein promotes nucleation in branched actin networks. Authors: Johanna Funk / Felipe Merino / Matthias Schaks / Klemens Rottner / Stefan Raunser / Peter Bieling / Abstract: Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside ...Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside from terminating filament growth, CP potentiates the nucleation of actin filaments by the Arp2/3 complex in branched actin networks through an unclear mechanism. Here, we combine structural biology with in vitro reconstitution to demonstrate that CP not only terminates filament elongation, but indirectly stimulates the activity of Arp2/3 activating nucleation promoting factors (NPFs) by preventing their association to filament barbed ends. Key to this function is one of CP's C-terminal "tentacle" extensions, which sterically masks the main interaction site of the terminal actin protomer. Deletion of the β tentacle only modestly impairs capping. However, in the context of a growing branched actin network, its removal potently inhibits nucleation promoting factors by tethering them to capped filament ends. End tethering of NPFs prevents their loading with actin monomers required for activation of the Arp2/3 complex and thus strongly inhibits branched network assembly both in cells and reconstituted motility assays. Our results mechanistically explain how CP couples two opposed processes-capping and nucleation-in branched actin network assembly. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13343.map.gz | 196.5 MB | EMDB map data format | |
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Header (meta data) | emd-13343-v30.xml emd-13343.xml | 26.1 KB 26.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13343_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_13343.png | 116.7 KB | ||
Masks | emd_13343_msk_1.map | 216 MB | Mask map | |
Others | emd_13343_additional_1.map.gz emd_13343_additional_2.map.gz emd_13343_half_map_1.map.gz emd_13343_half_map_2.map.gz | 185.2 MB 202.4 MB 104.3 MB 104.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13343 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13343 | HTTPS FTP |
-Validation report
Summary document | emd_13343_validation.pdf.gz | 437.5 KB | Display | EMDB validaton report |
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Full document | emd_13343_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | emd_13343_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_13343_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13343 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13343 | HTTPS FTP |
-Related structure data
Related structure data | 7pdzMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13343.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Locally filtered map with global B-factor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13343_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally filtered map using deepEMhancer's high resolution model
File | emd_13343_additional_1.map | ||||||||||||
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Annotation | Locally filtered map using deepEMhancer's high resolution model | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map filtered globally to a resolution of 3.9 A
File | emd_13343_additional_2.map | ||||||||||||
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Annotation | Map filtered globally to a resolution of 3.9 A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13343_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13343_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex between capping protein and the barbed end of cytoplasmic...
Entire | Name: Complex between capping protein and the barbed end of cytoplasmic actin filaments |
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Components |
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-Supramolecule #1: Complex between capping protein and the barbed end of cytoplasmic...
Supramolecule | Name: Complex between capping protein and the barbed end of cytoplasmic actin filaments type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Macromolecule #1: Isoform 2 of F-actin-capping protein subunit beta
Macromolecule | Name: Isoform 2 of F-actin-capping protein subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 30.669768 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK ...String: MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK LTSTVMLWLQ TNKSGSGTMN LGGSLTRQME KDETVSDCSP HIANIGRLVE DMENKIRSTL NEIYFGKTKD IV NGLRSVQ TFADKSKQEA LKNDLVEALK RKQQC |
-Macromolecule #2: F-actin-capping protein subunit alpha-1
Macromolecule | Name: F-actin-capping protein subunit alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 32.980703 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MADFEDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY DDQVLITEHG DLGNSRFLD PRNQISFKFD HLRKEASDPQ PEDVDGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF ...String: MADFEDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY DDQVLITEHG DLGNSRFLD PRNQISFKFD HLRKEASDPQ PEDVDGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF WNGRWRSEWK FTITPPSAQV VGVLKIQVHY YEDGNVQLVS HKDVQDSVTV SNEVQTTKEF IKIIESAENE YQ TAISENY QTMSDTTFKA LRRQLPVTRT KIDWNKILSY KIGKEMQNA |
-Macromolecule #3: Actin, cytoplasmic 1
Macromolecule | Name: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Bovine (cattle) |
Molecular weight | Theoretical: 41.79568 KDa |
Sequence | String: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG ...String: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF |
-Macromolecule #4: Phalloidin
Macromolecule | Name: Phalloidin / type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 808.899 Da |
Sequence | String: (HYP)AW(EEP)A(DTH)C |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 Component:
Details: KMEI buffer | |||||||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Mild discharging with 5 mA current | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 4204 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |