+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22416 | ||||||||||||
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Title | Cryo-EM structure of Arpin-bound Arp2/3 complex | ||||||||||||
Map data | Map of bovine Arp2/3 complex with Arpin CA peptide. Postprocessed with deepEMhancer | ||||||||||||
Sample |
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Keywords | actin / ATPase / actin related protein / arp / cytoskeleton / Arp2-3 complex / actin nucleation / actin branching / CONTRACTILE PROTEIN / Arpin | ||||||||||||
Function / homology | Function and homology information negative regulation of actin nucleation / negative regulation of lamellipodium morphogenesis / 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 / directional locomotion / regulation of actin filament polymerization / Clathrin-mediated endocytosis ...negative regulation of actin nucleation / negative regulation of lamellipodium morphogenesis / 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 / directional locomotion / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / cilium assembly / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / negative regulation of cell migration / cell projection / structural constituent of cytoskeleton / actin filament binding / cell migration / lamellipodium / site of double-strand break / actin binding / cell cortex / neuron projection / synapse / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 Å | ||||||||||||
Authors | van Eeuwen T / Fregoso FE | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular mechanism of Arp2/3 complex inhibition by Arpin. Authors: Fred E Fregoso / Trevor van Eeuwen / Gleb Simanov / Grzegorz Rebowski / Malgorzata Boczkowska / Austin Zimmet / Alexis M Gautreau / Roberto Dominguez / Abstract: Positive feedback loops involving signaling and actin assembly factors mediate the formation and remodeling of branched actin networks in processes ranging from cell and organelle motility to ...Positive feedback loops involving signaling and actin assembly factors mediate the formation and remodeling of branched actin networks in processes ranging from cell and organelle motility to mechanosensation. The Arp2/3 complex inhibitor Arpin controls the directional persistence of cell migration by interrupting a feedback loop involving Rac-WAVE-Arp2/3 complex, but Arpin's mechanism of inhibition is unknown. Here, we describe the cryo-EM structure of Arpin bound to Arp2/3 complex at 3.24-Å resolution. Unexpectedly, Arpin binds Arp2/3 complex similarly to WASP-family nucleation-promoting factors (NPFs) that activate the complex. However, whereas NPFs bind to two sites on Arp2/3 complex, on Arp2-ArpC1 and Arp3, Arpin only binds to the site on Arp3. Like NPFs, Arpin has a C-helix that binds at the barbed end of Arp3. Mutagenesis studies in vitro and in cells reveal how sequence differences within the C-helix define the molecular basis for inhibition by Arpin vs. activation by NPFs. | ||||||||||||
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_22416.map.gz | 110.8 MB | EMDB map data format | |
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Header (meta data) | emd-22416-v30.xml emd-22416.xml | 33 KB 33 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22416_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_22416.png | 235.5 KB | ||
Filedesc metadata | emd-22416.cif.gz | 8.6 KB | ||
Others | emd_22416_additional_1.map.gz emd_22416_half_map_1.map.gz emd_22416_half_map_2.map.gz | 117.9 MB 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22416 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22416 | HTTPS FTP |
-Validation report
Summary document | emd_22416_validation.pdf.gz | 735.7 KB | Display | EMDB validaton report |
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Full document | emd_22416_full_validation.pdf.gz | 735.3 KB | Display | |
Data in XML | emd_22416_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_22416_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22416 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22416 | HTTPS FTP |
-Related structure data
Related structure data | 7jpnMC 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_22416.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of bovine Arp2/3 complex with Arpin CA peptide. Postprocessed with deepEMhancer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.836 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Map of bovine Arp2/3 complex with Arpin CA...
File | emd_22416_additional_1.map | ||||||||||||
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Annotation | Map of bovine Arp2/3 complex with Arpin CA peptide. B factor sharpend and postprocessed with deepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of bovine Arp2/3 complex with Arpin CA peptide.
File | emd_22416_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of bovine Arp2/3 complex with Arpin CA peptide. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of bovine Arp2/3 complex with Arpin CA peptide.
File | emd_22416_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of bovine Arp2/3 complex with Arpin CA peptide. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : bovine Arp2/3 complex with Arpin
+Supramolecule #1: bovine Arp2/3 complex with Arpin
+Supramolecule #2: bovine Arp2/3
+Supramolecule #3: Arpin
+Macromolecule #1: Actin-related protein 3
+Macromolecule #2: Actin-related protein 2
+Macromolecule #3: Actin-related protein 2/3 complex subunit 1B
+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: Arpin
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE
-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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Grid | Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: unspecified | ||||||||||||||||||
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 |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 132 / Target criteria: correlation | ||||||
Output model | PDB-7jpn: |