[English] 日本語
Yorodumi- EMDB-20711: Cryo-EM structure of cofilactin from partially cofilin-decorated ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20711 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of cofilactin from partially cofilin-decorated actin filaments. | |||||||||
Map data | Helical reconstruction of cofilactin from a partially decorated sample. The map has been masked and sharpened with a b-factor of -215. | |||||||||
Sample |
| |||||||||
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 / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / lamellipodium membrane / actin filament bundle assembly / striated muscle thin filament / mitotic cytokinesis / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / 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 / 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 / ruffle membrane / nuclear matrix / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / actin cytoskeleton organization / growth cone / cell body / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Huehn AR / Bibeau JP / Schramm AC / Cao W / De La Cruz EM / Sindelar CV | |||||||||
Funding support | United States, 2 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20711.map.gz | 5.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-20711-v30.xml emd-20711.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20711_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_20711.png | 49 KB | ||
Masks | emd_20711_msk_1.map | 40.6 MB | Mask map | |
Others | emd_20711_additional.map.gz emd_20711_additional_1.map.gz emd_20711_half_map_1.map.gz emd_20711_half_map_2.map.gz | 38.2 MB 38.2 MB 7.3 MB 7.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20711 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20711 | HTTPS FTP |
-Validation report
Summary document | emd_20711_validation.pdf.gz | 458.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_20711_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | emd_20711_validation.xml.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20711 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20711 | HTTPS FTP |
-Related structure data
Related structure data | 6vaoMC 6ubyC 6uc0C 6uc4C 6vauC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_20711.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Helical reconstruction of cofilactin from a partially decorated sample. The map has been masked and sharpened with a b-factor of -215. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_20711_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unmasked final map.
File | emd_20711_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unmasked final map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unmasked final map.
File | emd_20711_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unmasked final map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Independently refined half map (2/2) of cofilactin from...
File | emd_20711_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Independently refined half map (2/2) of cofilactin from a partially decorated sample. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Independently refined half map (1/2) of cofilactin from...
File | emd_20711_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Independently refined half map (1/2) of cofilactin from a partially decorated sample. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of rabbit skeletal actin with human cofilin-1
Entire | Name: Complex of rabbit skeletal actin with human cofilin-1 |
---|---|
Components |
|
-Supramolecule #1: Complex of rabbit skeletal actin with human cofilin-1
Supramolecule | Name: Complex of rabbit skeletal actin with human cofilin-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|
-Supramolecule #2: Skeletal Actin
Supramolecule | Name: Skeletal Actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Supramolecule #3: Cofilin-1
Supramolecule | Name: Cofilin-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Rabbit Skeletal Actin
Macromolecule | Name: Rabbit Skeletal Actin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Sequence | String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG ...String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV MSGGTTMYPG IADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT KQEYDEAGPS IVHRKCF |
-Macromolecule #2: Human Cofilin-1
Macromolecule | Name: Human Cofilin-1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASGVAVSDG VIKVFNDMKV RKSSTPEEVK KRKKAVLFCL SEDKKNIILE EGKEILVGDV GQTVDDPYAT FVKMLPDKDC RYALYDATYE TKESKKEDLV FIFWAPESAP LKSKMIYASS KDAIKKKLTG IKHELQANCY EEVKDRCTLA EKLGGSAVIS LEGKPL |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.6 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | 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 |