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Yorodumi- EMDB-25707: Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25707 | ||||||||||||
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Title | Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation | ||||||||||||
Map data | Main map post processed with deepEMhancer | ||||||||||||
Sample |
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Keywords | actin / ATPase / actin related protein / arp / cytoskeleton / Arp2-3 complex / actin nucleation / actin branching / CONTRACTILE PROTEIN / CapZ | ||||||||||||
Function / homology | Function and homology information negative regulation of membrane tubulation / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / plasma membrane tubulation / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation ...negative regulation of membrane tubulation / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / plasma membrane tubulation / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / negative regulation of lymphocyte migration / actin nucleation / postsynapse organization / F-actin capping protein complex / WASH complex / negative regulation of filopodium assembly / regulation of cell projection assembly / vesicle organization / actin cap / postsynaptic actin cytoskeleton organization / vesicle transport along actin filament / regulation of actin filament polymerization / positive regulation of chemotaxis / Clathrin-mediated endocytosis / vesicle budding from membrane / cell junction assembly / COPI-independent Golgi-to-ER retrograde traffic / barbed-end actin filament capping / dendritic spine morphogenesis / protein-containing complex localization / actin polymerization or depolymerization / RHOF GTPase cycle / RHOD GTPase cycle / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of filopodium assembly / Neutrophil degranulation / regulation of postsynapse organization / cytoskeletal motor activator activity / cortical cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / cell leading edge / filamentous actin / actin filament bundle / brush border / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / Advanced glycosylation endproduct receptor signaling / skeletal muscle myofibril / cilium assembly / actin monomer binding / positive regulation of double-strand break repair via homologous recombination / COPI-mediated anterograde transport / positive regulation of lamellipodium assembly / skeletal muscle fiber development / stress fiber / titin binding / cytoskeleton organization / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cytoskeletal protein binding / MHC class II antigen presentation / actin filament polymerization / sarcomere / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / hippocampal mossy fiber to CA3 synapse / filopodium / cell projection / actin filament / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / cell migration / lamellipodium / regulation of protein localization / site of double-strand break / Factors involved in megakaryocyte development and platelet production / actin binding / cell cortex / actin cytoskeleton organization / cell body / cytoplasmic vesicle / protein-containing complex assembly / postsynapse / postsynaptic density / cytoskeleton / hydrolase activity / neuron projection / cadherin binding / protein domain specific binding Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) / Oryctolagus cuniculus (rabbit) / Homo sapiens (human) / cattle (cattle) / rabbit (rabbit) / Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Rebowski G / van Eeuwen T / Boczkowska M / Dominguez R | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of an Arp2/3 complex mini-branch capped by capping protein (CapZ) Authors: Rebowski G / van Eeuwen T / Dominguez R / Boczkowska M | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25707.map.gz | 146.5 MB | EMDB map data format | |
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Header (meta data) | emd-25707-v30.xml emd-25707.xml | 37.8 KB 37.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25707_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_25707.png | 90.7 KB | ||
Others | emd_25707_additional_1.map.gz emd_25707_additional_2.map.gz emd_25707_half_map_1.map.gz emd_25707_half_map_2.map.gz | 157.1 MB 83.1 MB 154.7 MB 154.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25707 | HTTPS FTP |
-Validation report
Summary document | emd_25707_validation.pdf.gz | 802.2 KB | Display | EMDB validaton report |
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Full document | emd_25707_full_validation.pdf.gz | 801.8 KB | Display | |
Data in XML | emd_25707_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_25707_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25707 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25707 | HTTPS FTP |
-Related structure data
Related structure data | 7t5qMC 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_25707.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map post processed with deepEMhancer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: map post processed with global b factor sharpening
File | emd_25707_additional_1.map | ||||||||||||
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Annotation | map post processed with global b factor sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_25707_additional_2.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_25707_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_25707_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : bovine Arp2/3 complex and Actin, CapZ
+Supramolecule #1: bovine Arp2/3 complex and Actin, CapZ
+Supramolecule #2: bovine Arp2/3
+Supramolecule #3: Actin skeletal muscle
+Supramolecule #4: F-actin-capping protein
+Macromolecule #1: Actin-related protein 3
+Macromolecule #2: Actin-related protein 2
+Macromolecule #3: Actin-related protein 2/3 complex subunit 1A
+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: Actin, alpha skeletal muscle
+Macromolecule #9: F-actin-capping protein subunit alpha-1/Actin nucleation-promotin...
+Macromolecule #10: F-actin-capping protein subunit beta/Actin nucleation-promoting f...
+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 | 5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC Details: Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger.. | ||||||||||||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Details | Data were collected in super-resolution mode with an illuminated area of 1.01 um, nominal dose of 40 e-/A^2, a dose rate of 4.87 e-/s/pixel, and 2 or 5 exposures per hole by image shift. |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 9661 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |