+Open data
-Basic information
Entry | Database: PDB / ID: 7jpn | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Arpin-bound Arp2/3 complex | ||||||||||||
Components |
| ||||||||||||
Keywords | CONTRACTILE PROTEIN / actin / ATPase / actin related protein / arp / cytoskeleton / Arp2-3 complex / actin nucleation / actin branching / 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 | Homo sapiens (human) Bos taurus (cattle) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å | ||||||||||||
Authors | van Eeuwen, T. / Fregoso, F.E. / Dominguez, R. / Zimmet, A. / Boczkowska, M. / Rebowski, G. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jpn.cif.gz | 346.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7jpn.ent.gz | 273.1 KB | Display | PDB format |
PDBx/mmJSON format | 7jpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jpn_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7jpn_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7jpn_validation.xml.gz | 68.2 KB | Display | |
Data in CIF | 7jpn_validation.cif.gz | 100.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/7jpn ftp://data.pdbj.org/pub/pdb/validation_reports/jp/7jpn | HTTPS FTP |
-Related structure data
Related structure data | 22416MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Actin-related protein ... , 7 types, 7 molecules ABCDEFG
#1: Protein | Mass: 46908.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61157 |
---|---|
#2: Protein | Mass: 42945.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A7MB62 |
#3: Protein | Mass: 41030.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q58CQ2 |
#4: Protein | Mass: 34402.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3MHR7 |
#5: Protein | Mass: 20572.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T035 |
#6: Protein | Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q148J6 |
#7: Protein | Mass: 15473.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: G3MXC8 |
-Protein/peptide , 1 types, 1 molecules H
#8: Protein/peptide | Mass: 3730.892 Da / Num. of mol.: 1 / Fragment: UNP residues 193-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPIN, C15orf38 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6K5 |
---|
-Non-polymers , 2 types, 4 molecules
#9: Chemical | #10: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.2489 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | ||||||||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE Details: Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS 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. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: -3500 nm / Nominal defocus min: -1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.6 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9661 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
Image processing | Details: Super resolution mode; micrographs binned during motion correction | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF correction was done in cryoSPARC for intial 2D classification and then repeated in CTFFIND4 (Relion) for classification and final reconstruction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4485066 / Details: Particles autopicked in cryoSPARC | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182324 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 132 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|