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Yorodumi- PDB-7aqk: Model of the actin filament Arp2/3 complex branch junction in cells -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aqk | ||||||
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Title | Model of the actin filament Arp2/3 complex branch junction in cells | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Actin / Arp2-3 complex / Cytoskeleton | ||||||
Function / homology | Function and homology information podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization ...podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / peripheral region of growth cone / muscle cell projection membrane / meiotic cytokinesis / apical ectoplasmic specialization / basal ectoplasmic specialization / lamellipodium organization / spindle localization / skeletal muscle fiber adaptation / leading edge of lamellipodium / Striated Muscle Contraction / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / hemidesmosome / actin filament network formation / asymmetric cell division / Arp2/3 complex-mediated actin nucleation / protein kinase C signaling / cellular response to rapamycin / postsynapse organization / podosome ring / actin cap / postsynaptic actin cytoskeleton organization / Regulation of actin dynamics for phagocytic cup formation / apical dendrite / negative regulation of axon extension / maintenance of cell polarity / Clathrin-mediated endocytosis / positive regulation of astrocyte differentiation / regulation of actin filament polymerization / : / positive regulation of dendritic spine morphogenesis / astrocyte differentiation / positive regulation of fibroblast migration / positive regulation of podosome assembly / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / response to steroid hormone / podosome / positive regulation of filopodium assembly / regulation of synaptic vesicle endocytosis / smooth muscle cell migration / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / mesenchyme migration / positive regulation of smooth muscle cell migration / cell leading edge / cellular response to platelet-derived growth factor stimulus / filamentous actin / brush border / skeletal muscle thin filament assembly / striated muscle thin filament / excitatory synapse / positive regulation of double-strand break repair via homologous recombination / cilium assembly / positive regulation of protein targeting to membrane / glutamate receptor binding / response to mechanical stimulus / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / skeletal muscle fiber development / stress fiber / cellular response to transforming growth factor beta stimulus / axon terminus / ruffle / cytoskeletal protein binding / cellular response to epidermal growth factor stimulus / positive regulation of neuron differentiation / actin filament polymerization / Neutrophil degranulation / secretory granule / filopodium / dendritic shaft / cell projection / meiotic cell cycle / actin filament / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cellular response to type II interferon / structural constituent of cytoskeleton / ruffle membrane / synaptic vesicle membrane / actin filament binding / cell-cell junction / cell migration Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9 Å | ||||||
Authors | Faessler, F. / Dimchev, G. / Hodirnau, V.V. / Wan, W. / Schur, F.K.M. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Authors: Florian Fäßler / Georgi Dimchev / Victor-Valentin Hodirnau / William Wan / Florian K M Schur / Abstract: The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves ...The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7aqk.cif.gz | 790 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqk.ent.gz | 505.9 KB | Display | PDB format |
PDBx/mmJSON format | 7aqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aqk_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7aqk_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7aqk_validation.xml.gz | 117.6 KB | Display | |
Data in CIF | 7aqk_validation.cif.gz | 205 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqk ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqk | HTTPS FTP |
-Related structure data
Related structure data | 11869MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Actin-related protein ... , 7 types, 7 molecules bacdefg
#1: Protein | Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: P61161*PLUS |
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#2: Protein | Mass: 47428.031 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus I259V / Source method: isolated from a natural source Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q99JY9*PLUS |
#3: Protein | Mass: 41016.738 Da / Num. of mol.: 1 Mutation: From Bos taurus to Mus Musculus V43N, Q44K, V58I, D63E, K109N, S154N, N213S, A229V, S256N, S274N, G277V, K278T, L296M, S313G, A216T, R360K Source method: isolated from a natural source Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9WV32*PLUS |
#4: Protein | Mass: 34402.043 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus Y84F, S90P / Source method: isolated from a natural source Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9CVB6*PLUS |
#5: Protein | Mass: 20572.666 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus I24L / Source method: isolated from a natural source Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9JM76*PLUS |
#6: Protein | Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: P59999*PLUS |
#7: Protein | Mass: 16295.317 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus D28E / Source method: isolated from a natural source Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9CPW4*PLUS |
-Protein , 1 types, 11 molecules hijklmnopqr
#8: Protein | Mass: 42096.953 Da / Num. of mol.: 11 / Source method: isolated from a natural source Details: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even ...Details: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: P68134*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Actin Filament Arp2/3 Complex Branch Junction / Type: CELL Details: Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||
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Source (natural) | Organism: Mus musculus (house mouse) / Cellular location: Lamellipodium | ||||||||||||||||||||||||
Buffer solution | pH: 6.1 / Details: Adjust to pH 6.1 using NaOH | ||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K Details: Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: -5.5 nm / Nominal defocus min: -1.75 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.21 sec. / Electron dose: 2.79 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) Details: Images were collected in movie-mode at 7 frames per tilt |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14296 Details: Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Method: Template Matching Details: After first classification in Dynamo and re-extraction in Warp 17,146 subvolumes remained. Num. of tomograms: 131 / Num. of volumes extracted: 39300 Reference model: Reference generated from manually selected particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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