- EMDB-20721: Isolated cofilin bound to an actin filament -
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Basic information
Entry
Database: EMDB / ID: EMD-20721
Title
Isolated cofilin bound to an actin filament
Map data
Final unmasked map of isolated, bound cofilin segments selected from partially cofilin-decorated actin filaments. This map was low-pass filtered to 7.8 A and sharpened with a B-factor of -200.
Sample
Complex: Complex of rabbit skeletal actin with isolated, bound human cofilin-1
Complex: Rabbit Skeletal Actin
Protein or peptide: Actin, alpha skeletal muscle
Complex: Human Cofilin-1
Protein or peptide: Cofilin-1
Ligand: MAGNESIUM ION
Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywords
Cytoskeleton / STRUCTURAL PROTEIN
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM097348
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM110533001
United States
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
Deposition
Sep 13, 2019
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Header (metadata) release
Jan 1, 2020
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Map release
Jan 1, 2020
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Update
Mar 20, 2024
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Current status
Mar 20, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_20721.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Final unmasked map of isolated, bound cofilin segments selected from partially cofilin-decorated actin filaments. This map was low-pass filtered to 7.8 A and sharpened with a B-factor of -200.
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 1117338 Details: Both bare and cofilin-decorated segments were selected and initially refined together.
Startup model
Type of model: OTHER
Final reconstruction
Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF Details: Filament segments with isolated, bound cofilin were split into even and odd halves for FSC calculations. Number images used: 8917
Initial angle assignment
Type: NOT APPLICABLE
Final angle assignment
Type: NOT APPLICABLE
Final 3D classification
Number classes: 2 / Avg.num./class: 559000 Details: Particle subtraction and masking were used to restrict classification to a single subunit per boxed segment. Particles were sorted into a bare and cofilin-decorated class. Filaments were ...Details: Particle subtraction and masking were used to restrict classification to a single subunit per boxed segment. Particles were sorted into a bare and cofilin-decorated class. Filaments were then searched for isolated, bound cofilin.
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