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Yorodumi- EMDB-21502: Structure of Dip1-activated Arp2/3 complex with nucleated actin f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21502 | |||||||||
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Title | Structure of Dip1-activated Arp2/3 complex with nucleated actin filament | |||||||||
Map data | Dip1 activated Arp2/3 complex with nucleated actin filament composite focused map | |||||||||
Sample |
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Function / homology | Function and homology information protein localization to actin cortical patch / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Clathrin-mediated endocytosis / actin cortical patch organization / Neutrophil degranulation / medial cortex / actin cortical patch localization / cell cortex of cell tip / positive regulation of Arp2/3 complex-mediated actin nucleation ...protein localization to actin cortical patch / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Clathrin-mediated endocytosis / actin cortical patch organization / Neutrophil degranulation / medial cortex / actin cortical patch localization / cell cortex of cell tip / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / cell tip / actin cortical patch / regulation of actin filament polymerization / cell septum / mating projection tip / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / establishment or maintenance of cell polarity / tropomyosin binding / mesenchyme migration / cell division site / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / mitotic cytokinesis / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / actin filament binding / endocytosis / calcium-dependent protein binding / lamellipodium / cell cortex / cell body / toxin activity / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) / Fission yeast (fission yeast) / Rabbit (rabbit) / death cap (death cap) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Shaaban M / Nolen BJ / Chowdhury S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state. Authors: Mohammed Shaaban / Saikat Chowdhury / Brad J Nolen / Abstract: Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the ...Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the nucleation-competent state is unclear due to lack of high-resolution structures of the activated state. Here we report a ~3.9 Å resolution cryo-EM structure of activated Schizosaccharomyces pombe Arp2/3 complex bound to the S. pombe NPF Dip1 and attached to the end of the nucleated actin filament. The structure reveals global and local conformational changes that allow the two actin-related proteins in Arp2/3 complex to mimic a filamentous actin dimer and template nucleation. Activation occurs through a clamp-twisting mechanism, in which Dip1 forces two core subunits in Arp2/3 complex to pivot around one another, shifting half of the complex into a new activated position. By showing how Dip1 stimulates activation, the structure reveals how NPFs can activate Arp2/3 complex in diverse cellular processes. | |||||||||
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_21502.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-21502-v30.xml emd-21502.xml | 38.8 KB 38.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21502_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_21502.png | 126 KB | ||
Masks | emd_21502_msk_1.map | 59.6 MB | Mask map | |
Others | emd_21502_additional_1.map.gz emd_21502_additional_2.map.gz emd_21502_additional_3.map.gz emd_21502_half_map_1.map.gz emd_21502_half_map_2.map.gz | 3.4 MB 3 MB 8.4 MB 55.7 MB 55.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21502 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21502 | HTTPS FTP |
-Validation report
Summary document | emd_21502_validation.pdf.gz | 687.3 KB | Display | EMDB validaton report |
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Full document | emd_21502_full_validation.pdf.gz | 686.9 KB | Display | |
Data in XML | emd_21502_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_21502_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21502 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21502 | HTTPS FTP |
-Related structure data
Related structure data | 6w17MC 6w18C C: citing same article (ref.) M: atomic model generated by this map |
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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_21502.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Dip1 activated Arp2/3 complex with nucleated actin filament composite focused map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.10972 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_21502_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Focused map of Arps and actin filament
File | emd_21502_additional_1.map | ||||||||||||
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Annotation | Focused map of Arps and actin filament | ||||||||||||
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Density Histograms |
-Additional map: Focused map of Dip1 Arp2/3 complex
File | emd_21502_additional_2.map | ||||||||||||
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Annotation | Focused map of Dip1 Arp2/3 complex | ||||||||||||
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Density Histograms |
-Additional map: Dip1 activated Arp2/3 complex with nucleated actin filament...
File | emd_21502_additional_3.map | ||||||||||||
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Annotation | Dip1 activated Arp2/3 complex with nucleated actin filament unsharpened, non-filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_21502_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
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Density Histograms |
-Half map: half map 2
File | emd_21502_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex consisting of actin-filament nucleator, Arp2/3 complex as...
+Supramolecule #1: Complex consisting of actin-filament nucleator, Arp2/3 complex as...
+Macromolecule #1: Actin-related protein 3
+Macromolecule #2: Actin-related protein 2
+Macromolecule #3: Actin-related protein 2/3 complex subunit 1
+Macromolecule #4: Actin-related protein 2/3 complex subunit 2
+Macromolecule #5: Actin-related protein 2/3 complex subunit 3
+Macromolecule #6: Actin-related protein 2/3 complex subunit 4
+Macromolecule #7: Actin-related protein 2/3 complex subunit 5
+Macromolecule #8: Protein dip1
+Macromolecule #9: Actin, alpha skeletal muscle
+Macromolecule #10: Phalloidin
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: 20mA current | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Details | Data were collected by stage shifting to targeted exposure positions. |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 2 / Number real images: 5109 / Average exposure time: 60.0 sec. / Average electron dose: 36.35 e/Å2 Details: Each micrograph was collected as dose-fractionated movies consisting of 45 fractions per movie. |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.75 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 92000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |