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- PDB-7aqk: Model of the actin filament Arp2/3 complex branch junction in cells -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aqk | ||||||
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Title | Model of the actin filament Arp2/3 complex branch junction in cells | ||||||
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Function / homology | ![]() 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 / : / meiotic cytokinesis / muscle cell projection membrane / apical ectoplasmic specialization / basal ectoplasmic specialization / cellular response to rapamycin / lamellipodium organization / spindle localization / skeletal muscle fiber adaptation / cellular response to trichostatin A / leading edge of lamellipodium / Striated Muscle Contraction / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
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Method | ![]() ![]() | ||||||
![]() | Faessler, F. / Dimchev, G. / Hodirnau, V.V. / Wan, W. / Schur, F.K.M. | ||||||
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 790 KB | Display | ![]() |
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PDB format | ![]() | 505.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11869MC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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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) ![]() ![]() ![]() |
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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) ![]() ![]() ![]() |
#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) ![]() ![]() ![]() |
#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) ![]() ![]() ![]() |
#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) ![]() ![]() ![]() |
#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) ![]() ![]() ![]() |
#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) ![]() ![]() ![]() |
-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) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||
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![]() ![]() | ||||||||||||||||||||||||
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 |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
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![]() |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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