+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19503 | ||||||||||||
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Title | Structure of the F-actin barbed end bound by formin mDia1 | ||||||||||||
Map data | Sharpened cryo-EM density map of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
Sample |
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Keywords | actin / formin / Cdc12 / profilin / actin assembly / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information negative regulation of neuron projection regeneration / multicellular organismal locomotion / MGMT-mediated DNA damage reversal / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase ...negative regulation of neuron projection regeneration / multicellular organismal locomotion / MGMT-mediated DNA damage reversal / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / actin nucleation / positive regulation of norepinephrine uptake / neuron projection retraction / cellular response to cytochalasin B / DNA-methyltransferase activity / bBAF complex / npBAF complex / RHO GTPases Activate Formins / protein localization to microtubule / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / profilin binding / morphogenesis of a polarized epithelium / cellular response to histamine / GBAF complex / postsynaptic actin cytoskeleton / protein localization to adherens junction / Formation of annular gap junctions / regulation of G0 to G1 transition / dense body / Gap junction degradation / Tat protein binding / DNA alkylation repair / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of double-strand break repair / DNA ligation / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / regulation of microtubule-based process / regulation of release of sequestered calcium ion into cytosol / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / axon midline choice point recognition / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / regulation of cytoskeleton organization / apical junction complex / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / cortical cytoskeleton / nitric-oxide synthase binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / brush border / kinesin binding / calyx of Held / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / actin filament polymerization / Neutrophil degranulation / axonogenesis / negative regulation of protein binding / cell motility / methyltransferase activity / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of transmembrane transporter activity / positive regulation of cell differentiation / sensory perception of sound / FCGR3A-mediated phagocytosis Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | ||||||||||||
Authors | Oosterheert W / Boiero Sanders M / Funk J / Prumbaum D / Raunser S / Bieling P | ||||||||||||
Funding support | Germany, European Union, 3 items
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Citation | Journal: Science / Year: 2024 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 | emd_19503.map.gz | 398.6 MB | EMDB map data format | |
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Header (meta data) | emd-19503-v30.xml emd-19503.xml | 27.3 KB 27.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19503_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_19503.png | 95.5 KB | ||
Masks | emd_19503_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-19503.cif.gz | 8 KB | ||
Others | emd_19503_additional_1.map.gz emd_19503_half_map_1.map.gz emd_19503_half_map_2.map.gz | 209.9 MB 390.9 MB 390.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19503 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19503 | HTTPS FTP |
-Related structure data
Related structure data | 8ru2MC 8rtyC 8ru0C 8rv2C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19503.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened cryo-EM density map of the F-actin barbed end bound by the formin mDia1 | ||||||||||||||||||||
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
File | emd_19503_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: 3D-refined, unsharpened cryo-EM density map of the F-actin...
File | emd_19503_additional_1.map | ||||||||||||
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Annotation | 3D-refined, unsharpened cryo-EM density map of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1 of the F-actin barbed...
File | emd_19503_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map 1 of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 2 of the F-actin barbed...
File | emd_19503_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 2 of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mDia1-bound F-actin barbed end.
Entire | Name: mDia1-bound F-actin barbed end. |
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Components |
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-Supramolecule #1: mDia1-bound F-actin barbed end.
Supramolecule | Name: mDia1-bound F-actin barbed end. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Human beta-actin and mouse mDia1 were purified separately. Both proteins were mixed to assemble the complex prior to cryo-EM grid preparation. |
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-Supramolecule #2: Actin filament
Supramolecule | Name: Actin filament / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Mouse mDia1 (FH1FH2C domain)
Supramolecule | Name: Mouse mDia1 (FH1FH2C domain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Actin, cytoplasmic 1, N-terminally processed
Macromolecule | Name: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 1 Details: Human beta-actin was recombinantly purified from BTI-Tnao38 cells. Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.632422 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ...String: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLE K SYELPDGQVI TIGNERFRCP EALFQPSFLG MESAGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEI TALAPSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF UniProtKB: Actin, cytoplasmic 1 |
-Macromolecule #2: Methylated-DNA--protein-cysteine methyltransferase,Protein diapha...
Macromolecule | Name: Methylated-DNA--protein-cysteine methyltransferase,Protein diaphanous homolog 1 type: protein_or_peptide / ID: 2 / Details: Has a N-terminal snap-tag. / Number of copies: 2 / Enantiomer: LEVO EC number: methylated-DNA-[protein]-cysteine S-methyltransferase |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 86.469258 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASTMDIKLT GEFAMDKDCE MKRTTLDSPL GKLELSGCEQ GLHEIKLLGK GTSAADAVEV PAPAAVLGGP EPLMQATAWL NAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYQ QLAALAGNPA ATAAVKTALS GNPVPILIPC H RVVSSSGA ...String: MASTMDIKLT GEFAMDKDCE MKRTTLDSPL GKLELSGCEQ GLHEIKLLGK GTSAADAVEV PAPAAVLGGP EPLMQATAWL NAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYQ QLAALAGNPA ATAAVKTALS GNPVPILIPC H RVVSSSGA VGGYEGGLAV KEWLLAHEGH RLGKPGLGPA GGSPGGGSGG SEMASLSAVV VAPSVSSSAA VPPAPPLPGD SG TVIPPPP PGMGVPPPPP FGFGVPAAPV LPFGLTPKKV YKPEVQLRRP NWSKFVAEDL SQDCFWTKVK EDRFENNELF AKL TLAFSA QTKTSKAKKD QEGGEEKKSV QKKKVKELKV LDSKTAQNLS IFLGSFRMPY QEIKNVILEV NEAVLTESMI QNLI KQMPE PEQLKMLSEL KEEYDDLAES EQFGVVMGTV PRLRPRLNAI LFKLQFSEQV ENIKPEIVSV TAACEELRKS ENFSS LLEL TLLVGNYMNA GSRNAGAFGF NISFLCKLRD TKSADQKMTL LHFLAELCEN DHPEVLKFPD ELAHVEKASR VSAENL QKS LDQMKKQIAD VERDVQNFPA ATDEKDKFVE KMTSFVKDAQ EQYNKLRMMH SNMETLYKEL GDYFVFDPKK LSVEEFF MD LHNFRNMFLQ AVKENQKRRE TEEKMRRAKL AKEKAEKERL EKQQKREQLI DMNAEGDETG VMDSLLEALQ SGAAFRRK R GPRQVNRKAG CAVTSLLASE LTKDDAMAPG PVKVPKKSEG VPTILEEAKE LVGRASHHHH HH UniProtKB: Methylated-DNA--protein-cysteine methyltransferase, Protein diaphanous homolog 1, Protein diaphanous homolog 1 |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / 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: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.1 Component:
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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.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
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. |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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: 2 / Number real images: 38913 / Average electron dose: 67.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Details | Refinement performed using phenix real-space refine | |||||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT | |||||||||
Output model | PDB-8ru2: |