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Yorodumi- PDB-8f8t: Cryo-EM structure of the Tropomodulin-capped pointed end of F-actin -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f8t | ||||||||||||
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Title | Cryo-EM structure of the Tropomodulin-capped pointed end of F-actin | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Actin cytoskeleton / filament / Tmod | ||||||||||||
Function / homology | Function and homology information pointed-end actin filament capping / lens fiber cell development / myofibril assembly / Striated Muscle Contraction / cytoskeletal motor activator activity / myofibril / cortical cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / Striated Muscle Contraction / cytoskeletal motor activator activity / myofibril / cortical cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / muscle contraction / titin binding / actin filament polymerization / sarcomere / adult locomotory behavior / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin binding / cell body / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||||||||
Authors | Carman, P.J. / Barrie, K.R. / Dominguez, R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2023 Title: Structures of the free and capped ends of the actin filament. Authors: Peter J Carman / Kyle R Barrie / Grzegorz Rebowski / Roberto Dominguez / Abstract: The barbed and pointed ends of the actin filament (F-actin) are the sites of growth and shrinkage and the targets of capping proteins that block subunit exchange, including CapZ at the barbed end and ...The barbed and pointed ends of the actin filament (F-actin) are the sites of growth and shrinkage and the targets of capping proteins that block subunit exchange, including CapZ at the barbed end and tropomodulin at the pointed end. We describe cryo-electron microscopy structures of the free and capped ends of F-actin. Terminal subunits at the free barbed end adopt a "flat" F-actin conformation. CapZ binds with minor changes to the barbed end but with major changes to itself. By contrast, subunits at the free pointed end adopt a "twisted" monomeric actin (G-actin) conformation. Tropomodulin binding forces the second subunit into an F-actin conformation. The structures reveal how the ends differ from the middle in F-actin and how these differences control subunit addition, dissociation, capping, and interactions with end-binding proteins. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f8t.cif.gz | 545.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f8t.ent.gz | 452.4 KB | Display | PDB format |
PDBx/mmJSON format | 8f8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f8t_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8f8t_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8f8t_validation.xml.gz | 89 KB | Display | |
Data in CIF | 8f8t_validation.cif.gz | 130.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/8f8t ftp://data.pdbj.org/pub/pdb/validation_reports/f8/8f8t | HTTPS FTP |
-Related structure data
Related structure data | 28936MC 8f8pC 8f8qC 8f8rC 8f8sC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 42109.973 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Protein | | Mass: 40619.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMOD1, D9S57E, TMOD / Production host: Escherichia coli (E. coli) / References: UniProt: P28289 #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 |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 1.05 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: 278 K / Details: Blot force 0 Blot time 2.5 s |
-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: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 44.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1102793 / Details: Topaz particle picking with training | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25004 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||
Refine LS restraints |
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