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Open data
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Basic information
Entry | Database: PDB / ID: 9b27 | ||||||
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Title | Dia1 at the Barbed End of F-Actin | ||||||
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![]() | CYTOSOLIC PROTEIN / Actin / Filament / Elongation / Ends | ||||||
Function / homology | ![]() negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / actin nucleation / neuron projection retraction ...negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / actin nucleation / neuron projection retraction / RHO GTPases Activate Formins / profilin binding / regulation of microtubule-based process / axon midline choice point recognition / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / brush border / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / synaptic vesicle endocytosis / skeletal muscle myofibril / actin monomer binding / ephrin receptor signaling pathway / skeletal muscle fiber development / stress fiber / titin binding / cytoskeleton organization / Neutrophil degranulation / actin filament polymerization / filopodium / actin filament / sensory perception of sound / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein localization / brain development / small GTPase binding / ruffle membrane / spindle / calcium-dependent protein binding / neuron projection development / presynapse / lamellipodium / actin binding / gene expression / regulation of cell shape / cell body / actin cytoskeleton organization / transmembrane transporter binding / hydrolase activity / positive regulation of cell migration / neuron projection / protein domain specific binding / centrosome / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å | ||||||
![]() | Palmer, N.J. / Barrie, K.R. / Dominguez, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanisms of actin filament severing and elongation by formins. Authors: Nicholas J Palmer / Kyle R Barrie / Roberto Dominguez / ![]() Abstract: Humans express fifteen formins, playing crucial roles in actin-based processes, such as cytokinesis, cell motility, and mechanotransduction . However, the lack of structures bound to the actin ...Humans express fifteen formins, playing crucial roles in actin-based processes, such as cytokinesis, cell motility, and mechanotransduction . However, the lack of structures bound to the actin filament (F-actin) has been a major impediment to understanding formin function. While formins are known for their ability to nucleate and elongate F-actin , some formins can additionally depolymerize, sever, or bundle F-actin. Two mammalian formins, inverted formin-2 (INF2) and diaphanous-1 (Dia1), exemplify this diversity. INF2 displays potent severing activity but elongates weakly , whereas Dia1 has potent elongation activity but does not sever . Using cryo-electron microscopy (cryo-EM), we reveal five structural states of INF2 and two of Dia1 bound to the middle and barbed end of F-actin. INF2 and Dia1 bind differently to these sites, consistent with their distinct activities. The FH2 and WH2 domains of INF2 are positioned to sever F-actin, whereas Dia1 appears unsuited for severing. Structures also show how profilin-actin is delivered to the fast-growing barbed end, and how this is followed by a transition of the incoming monomer into the F-actin conformation and the release of profilin. Combined, the seven structures presented here provide step-by-step visualization of the mechanisms of F-actin severing and elongation by formins. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 520 KB | Display | ![]() |
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PDB format | ![]() | 430.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 92.8 KB | Display | |
Data in CIF | ![]() | 135.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 44099MC ![]() 9az4C ![]() 9azpC ![]() 9azqC ![]() 9b03C ![]() 9b0kC ![]() 9b3dC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 41387.227 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Protein | Mass: 49189.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
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Specimen | Conc.: 1.48 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
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Particle selection | Num. of particles selected: 112565 | |||||||||||||||||||||
3D reconstruction | Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36931 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1
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Refinement | Highest resolution: 3.51 Å |