+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6844 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cofilin decorated actin filament | ||||||||||||
Map data | Cofilin-decorated actin filament | ||||||||||||
Sample |
| ||||||||||||
Keywords | Actin / Cofilin / CYTOSOLIC PROTEIN / muscle / cytoskeleton | ||||||||||||
Function / homology | Function and homology information actin filament fragmentation / Striated Muscle Contraction / actin filament severing / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix ...actin filament fragmentation / Striated Muscle Contraction / actin filament severing / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Gallus gallus (chicken) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Tanaka K / Narita A | ||||||||||||
Funding support | Japan, 3 items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for cofilin binding and actin filament disassembly. Authors: Kotaro Tanaka / Shuichi Takeda / Kaoru Mitsuoka / Toshiro Oda / Chieko Kimura-Sakiyama / Yuichiro Maéda / Akihiro Narita / Abstract: Actin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin ...Actin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin (cofilin-decorated actin filament). The actin subunit structure of cofilactin (C-form) is distinct from those of F-actin (F-form) and monomeric actin (G-form). During the transition between these three conformations, the inner domain of actin (subdomains 3 and 4) and the majority of subdomain 1 move as two separate rigid bodies. The cofilin-actin interface consists of three distinct parts. Based on the rigid body movements of actin and the three cofilin-actin interfaces, we propose models for the cooperative binding of cofilin to actin, preferential binding of cofilin to ADP-bound actin filaments and cofilin-mediated severing of actin filaments. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6844.map.gz | 7.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6844-v30.xml emd-6844.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6844_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_6844.png | 204.2 KB | ||
Filedesc metadata | emd-6844.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6844 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6844 | HTTPS FTP |
-Validation report
Summary document | emd_6844_validation.pdf.gz | 438.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6844_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | emd_6844_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_6844_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6844 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6844 | HTTPS FTP |
-Related structure data
Related structure data | 5yu8MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6844.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cofilin-decorated actin filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Cofilin-decorated actin filament
Entire | Name: Cofilin-decorated actin filament |
---|---|
Components |
|
-Supramolecule #1: Cofilin-decorated actin filament
Supramolecule | Name: Cofilin-decorated actin filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Gallus gallus (chicken) |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 41.875633 KDa |
Recombinant expression | Organism: Gallus gallus (chicken) |
Sequence | String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #2: Cofilin-2
Macromolecule | Name: Cofilin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 18.690598 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASGVTVNDE VIKVFNDMKV RKSSTPEEIK KRKKAVLFCL SDDKKQIIVE EAKQILVGDI GDTVEDPYTA FVKLLPLNDC RYALYDATY ETKESKKEDL VFIFWAPESA PLKSKMIYAS SKDAIKKKFT GIKHEWQVNG LDDIKDRSTL GEKLGGNVVV S LEGKPL UniProtKB: Cofilin-2 |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.5 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 24.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |