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- EMDB-16887: Cryo-EM structure of the undecorated barbed end of filamentous be... -
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Open data
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Basic information
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Title | Cryo-EM structure of the undecorated barbed end of filamentous beta/gamma actin | ||||||||||||
![]() | 3D-refined, sharpened cryo-EM density map of the undecorated barbed end of F-actin. | ||||||||||||
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![]() | Actin filament / cytoskeletal protein / ATPase / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | ![]() Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / RHOF GTPase cycle / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs ...Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / RHOF GTPase cycle / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / DNA Damage Recognition in GG-NER / UCH proteinases / VEGFA-VEGFR2 Pathway / structural constituent of postsynaptic actin cytoskeleton / dense body / Clathrin-mediated endocytosis / NuA4 histone acetyltransferase complex / axonogenesis / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / cytoskeleton / hydrolase activity / axon / focal adhesion / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | ||||||||||||
![]() | Oosterheert W / Blanc FEC / Roy A / Belyy A / Hofnagel O / Hummer G / Bieling P / Raunser S | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Authors: Wout Oosterheert / Florian E C Blanc / Ankit Roy / Alexander Belyy / Micaela Boiero Sanders / Oliver Hofnagel / Gerhard Hummer / Peter Bieling / Stefan Raunser / ![]() Abstract: The release of inorganic phosphate (P) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. The mechanisms underlying P release ...The release of inorganic phosphate (P) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. The mechanisms underlying P release from the core and barbed end of actin filaments remain unclear. Here, using human and bovine actin isoforms, we combine cryo-EM with molecular-dynamics simulations and in vitro reconstitution to demonstrate how actin releases P through a 'molecular backdoor'. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and opens only transiently through concerted amino acid rearrangements. This explains why P escapes rapidly from the filament end but slowly from internal subunits. In a nemaline-myopathy-associated actin variant, the backdoor is predominantly open in filament-core subunits, resulting in accelerated P release and filaments with drastically shortened ADP-P caps. Our results provide the molecular basis for P release from actin and exemplify how a disease-linked mutation distorts the nucleotide-state distribution and atomic structure of the filament. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 203.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.2 KB 24.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.6 KB | Display | ![]() |
Images | ![]() | 90.9 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() ![]() | 108.1 MB 200.4 MB 200.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 983.3 KB | Display | ![]() |
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Full document | ![]() | 982.9 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oi6MC ![]() 8oi8C ![]() 8oidC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3D-refined, sharpened cryo-EM density map of the undecorated barbed end of F-actin. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: 3D-refined, unsharpened cryo-EM density map of the undecorated...
File | emd_16887_additional_1.map | ||||||||||||
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Annotation | 3D-refined, unsharpened cryo-EM density map of the undecorated barbed end of F-actin. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of the refinement of the...
File | emd_16887_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of the refinement of the undecorated barbed end of F-actin. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of the refinement of the...
File | emd_16887_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of the refinement of the undecorated barbed end of F-actin. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : actin-phalloidin complex
Entire | Name: actin-phalloidin complex |
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Components |
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-Supramolecule #1: actin-phalloidin complex
Supramolecule | Name: actin-phalloidin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Actin was purified as monomer from bovine thymus. Short filaments were reconstituted in vitro to obtain the barbed end structure. |
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-Supramolecule #2: cytosolic beta-gamma actin
Supramolecule | Name: cytosolic beta-gamma actin / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: phalloidin
Supramolecule | Name: phalloidin / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Actin, cytoplasmic 1
Macromolecule | Name: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 41.79568 KDa |
Sequence | String: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG ...String: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF UniProtKB: Actin, cytoplasmic 1 |
-Macromolecule #2: PHALLOIDIN
Macromolecule | Name: PHALLOIDIN / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 808.899 Da |
Sequence | String: W(EEP)A(DTH)C(HYP)A |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.1 Component:
Details: 10 mM imidazole pH 7.1, 100 mM KCl, 2 mM MgCl2 and 1 mM EGTA | |||||||||||||||
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Sample was directly collected from size-exclusion chromatography fractions. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Details | Microsope alignment was performed using SHERPA (Thermo Fisher) |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 1316 / Average exposure time: 4.0 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: c / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Real space refinement in phenix. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-8oi6: |