+Open data
-Basic information
Entry | Database: PDB / ID: 6uc0 | |||||||||
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Title | Isolated S3D-cofilin bound to an actin filament | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Cytoskeleton | |||||||||
Function / homology | Function and homology information actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / cytoskeletal motor activator activity ...actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / lamellipodium membrane / striated muscle thin filament / actin filament bundle assembly / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / mitotic cytokinesis / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / cytoskeleton organization / EPHB-mediated forward signaling / actin filament polymerization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / actin filament / ruffle membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to virus / Regulation of actin dynamics for phagocytic cup formation / nuclear matrix / actin filament binding / calcium-dependent protein binding / actin cytoskeleton / Platelet degranulation / lamellipodium / cell body / growth cone / actin cytoskeleton organization / vesicle / hydrolase activity / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / magnesium ion binding / extracellular space / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Huehn, A.R. / Bibeau, J.P. / Schramm, A.C. / Cao, W. / De La Cruz, E.M. / Sindelar, C.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Structures of cofilin-induced structural changes reveal local and asymmetric perturbations of actin filaments. Authors: Andrew R Huehn / Jeffrey P Bibeau / Anthony C Schramm / Wenxiang Cao / Enrique M De La Cruz / Charles V Sindelar / Abstract: Members of the cofilin/ADF family of proteins sever actin filaments, increasing the number of filament ends available for polymerization or depolymerization. Cofilin binds actin filaments with ...Members of the cofilin/ADF family of proteins sever actin filaments, increasing the number of filament ends available for polymerization or depolymerization. Cofilin binds actin filaments with positive cooperativity, forming clusters of contiguously bound cofilin along the filament lattice. Filament severing occurs preferentially at boundaries between bare and cofilin-decorated (cofilactin) segments and is biased at 1 side of a cluster. A molecular understanding of cooperative binding and filament severing has been impeded by a lack of structural data describing boundaries. Here, we apply methods for analyzing filament cryo-electron microscopy (cryo-EM) data at the single subunit level to directly investigate the structure of boundaries within partially decorated cofilactin filaments. Subnanometer resolution maps of isolated, bound cofilin molecules and an actin-cofilactin boundary indicate that cofilin-induced actin conformational changes are local and limited to subunits directly contacting bound cofilin. An isolated, bound cofilin compromises longitudinal filament contacts of 1 protofilament, consistent with a single cofilin having filament-severing activity. An individual, bound phosphomimetic (S3D) cofilin with weak severing activity adopts a unique binding mode that does not perturb actin structure. Cofilin clusters disrupt both protofilaments, consistent with a higher severing activity at boundaries compared to single cofilin. Comparison of these structures indicates that this disruption is substantially greater at pointed end sides of cofilactin clusters than at the barbed end. These structures, with the distribution of bound cofilin clusters, suggest that maximum binding cooperativity is achieved when 2 cofilins occupy adjacent sites. These results reveal the structural origins of cooperative cofilin binding and actin filament severing. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6uc0.cif.gz | 468.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uc0.ent.gz | 390.7 KB | Display | PDB format |
PDBx/mmJSON format | 6uc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uc0_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6uc0_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6uc0_validation.xml.gz | 94.8 KB | Display | |
Data in CIF | 6uc0_validation.cif.gz | 134.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/6uc0 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/6uc0 | HTTPS FTP |
-Related structure data
Related structure data | 20724MC 6ubyC 6uc4C 6vaoC 6vauC 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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1 |
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-Components
#1: Protein | Mass: 42096.953 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Protein | | Mass: 18560.541 Da / Num. of mol.: 1 / Mutation: S3D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Production host: Escherichia coli (E. coli) / References: UniProt: P23528 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ADP / Has ligand of interest | N | Sequence details | The molecules in the experiments were: Rabbit actin (UniProt P68135) and Human cofilin-1 (UniProt ...The molecules in the experiments were: Rabbit actin (UniProt P68135) and Human cofilin-1 (UniProt P23528), however the sequences modeled in the coordinates correspond to the sequences from Chicken actin and Chicken cofilin-2 since those were pdb models of homolog molecules used to fit into the cryo-EM density maps. | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 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) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: UCSF Chimera / Category: model fitting | ||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Particle selection | Num. of particles selected: 217500 Details: Both bare and S3D-cofilin-decorated filament segments were selected and initially refined together. | ||||||||||||||||||
3D reconstruction | Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20082 Details: Segments with isolated, bound S3D-cofilin were split into even and odd halves for FSC calculations. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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