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Open data
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Basic information
Entry | Database: PDB / ID: 6m5g | |||||||||
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Title | F-actin-Utrophin complex | |||||||||
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![]() | CONTRACTILE PROTEIN / Utrophin / N-terminus actin binding domain / calponin homology / F-actin / F-actin marker protein | |||||||||
Function / homology | ![]() synaptic signaling / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transporter activity / Striated Muscle Contraction / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / muscle organ development / positive regulation of cell-matrix adhesion / skeletal muscle thin filament assembly ...synaptic signaling / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transporter activity / Striated Muscle Contraction / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / muscle organ development / positive regulation of cell-matrix adhesion / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / filopodium / muscle contraction / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / neuromuscular junction / sarcolemma / integrin binding / actin binding / postsynaptic membrane / cytoskeleton / hydrolase activity / protein kinase binding / protein-containing complex / zinc ion binding / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Kumari, A. / Ragunath, V.K. / Sirajuddin, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into actin filament recognition by commonly used cellular actin markers. Authors: Archana Kumari / Shubham Kesarwani / Manjunath G Javoor / Kutti R Vinothkumar / Minhajuddin Sirajuddin / ![]() Abstract: Cellular studies of filamentous actin (F-actin) processes commonly utilize fluorescent versions of toxins, peptides, and proteins that bind actin. While the choice of these markers has been largely ...Cellular studies of filamentous actin (F-actin) processes commonly utilize fluorescent versions of toxins, peptides, and proteins that bind actin. While the choice of these markers has been largely based on availability and ease, there is a severe dearth of structural data for an informed judgment in employing suitable F-actin markers for a particular requirement. Here, we describe the electron cryomicroscopy structures of phalloidin, lifeAct, and utrophin bound to F-actin, providing a comprehensive high-resolution structural comparison of widely used actin markers and their influence towards F-actin. Our results show that phalloidin binding does not induce specific conformational change and lifeAct specifically recognizes closed D-loop conformation, i.e., ADP-Pi or ADP states of F-actin. The structural models aided designing of minimal utrophin and a shorter lifeAct, which can be utilized as F-actin marker. Together, our study provides a structural perspective, where the binding sites of utrophin and lifeAct overlap with majority of actin-binding proteins and thus offering an invaluable resource for researchers in choosing appropriate actin markers and generating new marker variants. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 397.2 KB | Display | ![]() |
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PDB format | ![]() | 314.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 101.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30085MC ![]() 7bt7C ![]() 7bteC ![]() 7btiC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 42096.953 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 30771.949 Da / Num. of mol.: 3 / Fragment: calponin domain 1, calponin domain 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P46939 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ADP / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||
Specimen | Conc.: 0.0002 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K / Details: blot for 3 seconds |
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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: OTHER / Nominal magnification: 59000 X / Nominal defocus max: 4735 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 120 K / Temperature (min): 100 K |
Image recording | Average exposure time: 2 sec. / Electron dose: 42.6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 765 / Details: 20 |
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Processing
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EM software |
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CTF correction | Details: GCTF for CTF correction / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -166.6 ° / Axial rise/subunit: 27.5 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 259938 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149660 / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 177 / Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5ONV Pdb chain-ID: A / Accession code: 5ONV / Pdb chain residue range: 6-373 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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