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- EMDB-19497: Cryo-EM reconstruction of the formin Cdc12 bound to the barbed en... -
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Basic information
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Title | Cryo-EM reconstruction of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin) | ||||||||||||
![]() | Sharpened cryo-EM density map of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). | ||||||||||||
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![]() | actin / formin / Cdc12 / actin assembly. / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | ![]() F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / medial cortex / mitotic actomyosin contractile ring assembly / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / mitotic actomyosin contractile ring ...F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / medial cortex / mitotic actomyosin contractile ring assembly / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / mitotic actomyosin contractile ring / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / mating projection tip / Prefoldin mediated transfer of substrate to CCT/TriC / barbed-end actin filament capping / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / cell division site / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / actin filament bundle assembly / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / actin filament polymerization / axonogenesis / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / regulation of transmembrane transporter activity / adherens junction / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / tau protein binding / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / kinetochore / small GTPase binding / nuclear matrix / platelet aggregation / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.54 Å | ||||||||||||
![]() | Oosterheert W / Boiero Sanders M / Funk J / Prumbaum D / Raunser S / Bieling P | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of actin filament elongation by formins. Authors: Wout Oosterheert / Micaela Boiero Sanders / Johanna Funk / Daniel Prumbaum / Stefan Raunser / Peter Bieling / ![]() Abstract: Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action ...Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action remain unclear. In this work, we present high-resolution cryo-electron microscopy structures of F-actin barbed ends bound by three distinct formins, revealing a common asymmetric formin conformation imposed by the filament. Formation of new intersubunit contacts during actin polymerization sterically displaces formin and triggers its translocation. This "undock-and-lock" mechanism explains how actin-filament growth is coordinated with formin movement. Filament elongation speeds are controlled by the positioning and stability of actin-formin interfaces, which distinguish fast and slow formins. Furthermore, we provide a structure of the actin-formin-profilin ring complex, which resolves how profilin is rapidly released from the barbed end during filament elongation. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 13.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.1 KB 31.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.5 KB | Display | ![]() |
Images | ![]() | 82.9 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 97.3 MB 107.5 MB 113.7 MB 115.5 MB 98.5 MB 98.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 800.2 KB | Display | ![]() |
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Full document | ![]() | 799.8 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rttC ![]() 8rtyC ![]() 8ru0C ![]() 8ru2C ![]() 8rv2C 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 | Sharpened cryo-EM density map of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 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 formin...
File | emd_19497_additional_1.map | ||||||||||||
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Annotation | 3D-refined, unsharpened cryo-EM density map of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM map Cdc12 bound to phalloidin-stabilized F-actin (EMD-19496),...
File | emd_19497_additional_2.map | ||||||||||||
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Annotation | Cryo-EM map Cdc12 bound to phalloidin-stabilized F-actin (EMD-19496), resampled on the cryo-EM reconstruction that was obtained without phalloidin. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Power-adjusted map of actin-Cdc12 with phalloidin(EMD-19496), resampled on...
File | emd_19497_additional_3.map | ||||||||||||
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Annotation | Power-adjusted map of actin-Cdc12 with phalloidin(EMD-19496), resampled on the no-phalloidin map. Used to construct a difference map between the reconstructions with and without phalloidin. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Difference map between actin-Cdc12 reconstructions that were obtained...
File | emd_19497_additional_4.map | ||||||||||||
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Annotation | Difference map between actin-Cdc12 reconstructions that were obtained in the absence (this entry) and presence (EMD-19496) of the toxin phalloidin. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1 of the formin Cdc12...
File | emd_19497_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map 1 of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 2 of the formin Cdc12...
File | emd_19497_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 2 of the formin Cdc12 bound to the barbed end of F-actin (without phalloidin). | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the ...
Entire | Name: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of F-actin. |
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Components |
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-Supramolecule #1: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the ...
Supramolecule | Name: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of F-actin. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Human beta-actin and S. Pombe Cdc12 were purified separately. Both proteins were mixed to assemble the complex prior to cryo-EM grid preparation. |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: Actin filament
Supramolecule | Name: Actin filament / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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-Supramolecule #3: Dimeric FH2 domain of S. Pombe Cdc12
Supramolecule | Name: Dimeric FH2 domain of S. Pombe Cdc12 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: human cytoplasmic beta-actin
Macromolecule | Name: human cytoplasmic beta-actin / type: protein_or_peptide / ID: 1 Details: Actin purified recombinantly from BTI-Tnao38 cells. Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA ...String: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA LPHAILRLDL AGRDLTDYLM KILTERGYSF TTTAEREIVR DIKEKLCYVA LDFEQEMATA ASSSSLEKSY ELPDGQVITI GNERFRCPEA LFQPSFLGME SAGIHETTFN SIMKCDVDIR KDLYANTVLS GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ EYDESGPSIV HRKCF UniProtKB: Actin, cytoplasmic 1 |
-Macromolecule #2: S. pombe Cdc12
Macromolecule | Name: S. pombe Cdc12 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SKDDLHKTTG LTRRPTRRLK QMHWEKLNSG LEFTFWTGPS DEANKILETL HTSGVLDELD ESFAMKEAK TLVKKTCART DYMSSELQKL FGIHFHKLSH KNPNEIIRMI LHCDDSMNEC V EFLSSDKV LNQPKLKADL EPYRIDWANG GDLVNSEKDA SELSRWDYLY ...String: SKDDLHKTTG LTRRPTRRLK QMHWEKLNSG LEFTFWTGPS DEANKILETL HTSGVLDELD ESFAMKEAK TLVKKTCART DYMSSELQKL FGIHFHKLSH KNPNEIIRMI LHCDDSMNEC V EFLSSDKV LNQPKLKADL EPYRIDWANG GDLVNSEKDA SELSRWDYLY VRLIVDLGGY WN QRMNALK VKNIIETNYE NLVRQTKLIG RAALELRDSK VFKGLLYLIL YLGNYMNDYV RQA KGFAIG SLQRLPLIKN ANNTKSLLHI LDITIRKHFP QFDNFSPELS TVTEAAKLNI EAIE QECSE LIRGCQNLQI DCDSGALSDP TVFHPDDKIL SVILPWLMEG TKKMDFLKEH LRTMN TTLN NAMRYFGEQP NDPNSKNLFF KRVDSFIIDY SKARSDNLKS EEEEASQHRR LNLVN UniProtKB: Cell division control protein 12 |
-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: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP) | ||||||||||||||||||
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / 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: 3 seconds, force 0.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV / Details: Gatan energy filter. |
Details | 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12009 / Average electron dose: 64.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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