+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21503 | |||||||||
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Title | Structure of S. pombe Arp2/3 complex in inactive state | |||||||||
Map data | Map of S. pombe Arp2/3 complex in inactive state | |||||||||
Sample |
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Keywords | Arp2/3 / actin / cytoskeletal protein / actin regulator / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information 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 / cell cortex of cell tip / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation ...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 / cell cortex of cell tip / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / cell tip / actin cortical patch / regulation of actin filament polymerization / mating projection tip / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / cell division site / mitotic cytokinesis / actin filament polymerization / structural constituent of cytoskeleton / actin filament binding / endocytosis / cell cortex / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 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_21503.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-21503-v30.xml emd-21503.xml | 30.4 KB 30.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21503_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_21503.png | 150.4 KB | ||
Masks | emd_21503_msk_1.map | 61 MB | Mask map | |
Filedesc metadata | emd-21503.cif.gz | 8.1 KB | ||
Others | emd_21503_additional.map.gz emd_21503_half_map_1.map.gz emd_21503_half_map_2.map.gz | 4.7 MB 56.6 MB 56.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21503 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21503 | HTTPS FTP |
-Validation report
Summary document | emd_21503_validation.pdf.gz | 1008.3 KB | Display | EMDB validaton report |
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Full document | emd_21503_full_validation.pdf.gz | 1007.9 KB | Display | |
Data in XML | emd_21503_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_21503_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21503 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21503 | HTTPS FTP |
-Related structure data
Related structure data | 6w18MC 6w17C 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_21503.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of S. pombe Arp2/3 complex in inactive state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8757 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_21503_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map of S. pombe Arp2/3 complex in inactive state
File | emd_21503_additional.map | ||||||||||||
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Annotation | Unsharpened map of S. pombe Arp2/3 complex in inactive state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_21503_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_21503_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Arp2/3 complex
+Supramolecule #1: Arp2/3 complex
+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: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / 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 Details: 4 uL of sample was applied to freshly glow-discharged grid. Excess sample was manually blotted off with a dry Whatman No.1 filter paper for 5-7 seconds. Immediately after the blotting step ...Details: 4 uL of sample was applied to freshly glow-discharged grid. Excess sample was manually blotted off with a dry Whatman No.1 filter paper for 5-7 seconds. Immediately after the blotting step the sample containing grid was rapidly vitrified by plunge freezing into liquid ethane.. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Details | Data were collected by combining untilted and tilted (20, 30 and 40 degrees) images. Stage shifting to the targeted exposure position was used for navigation during data acquisition. |
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 / Number grids imaged: 3 / Number real images: 5309 / Average exposure time: 40.0 sec. / Average electron dose: 44.34 e/Å2 Details: Each micrograph was collected as dose-fractionated movies consisting of 62 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: -1.3 µm / Nominal defocus min: -0.7000000000000001 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |