+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44135 | |||||||||
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Title | Dia1 in the Middle of F-actin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Actin / Filament / Elongation / Ends / CYTOSOLIC PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation / RHOA GTPase cycle / neuron projection retraction ...negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation / RHOA GTPase cycle / neuron projection retraction / RHO GTPases Activate Formins / profilin binding / regulation of microtubule-based process / axon midline choice point recognition / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / brush border / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / synaptic vesicle endocytosis / actin monomer binding / ephrin receptor signaling pathway / skeletal muscle fiber development / stress fiber / titin binding / cytoskeleton organization / actin filament polymerization / Neutrophil degranulation / filopodium / actin filament / sensory perception of sound / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / brain development / small GTPase binding / spindle / ruffle membrane / calcium-dependent protein binding / neuron projection development / protein localization / lamellipodium / presynapse / regulation of cell shape / actin binding / gene expression / actin cytoskeleton organization / cell body / transmembrane transporter binding / hydrolase activity / positive regulation of cell migration / neuron projection / protein domain specific binding / centrosome / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||
Authors | Palmer NJ / Barrie KR / Dominguez R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Mechanisms of actin filament severing and elongation by formins. Authors: Nicholas J Palmer / Kyle R Barrie / Roberto Dominguez / Abstract: Humans express 15 formins that play crucial roles in actin-based processes, including cytokinesis, cell motility and mechanotransduction. However, the lack of structures bound to the actin filament ...Humans express 15 formins that play crucial roles in actin-based processes, including cytokinesis, cell motility and mechanotransduction. However, the lack of structures bound to the actin filament (F-actin) has been a major impediment to understanding formin function. Whereas formins are known for their ability to nucleate and elongate F-actin, some formins can additionally depolymerize, sever or bundle F-actin. Two mammalian formins, inverted formin 2 (INF2) and diaphanous 1 (DIA1, encoded by DIAPH1), exemplify this diversity. INF2 shows potent severing activity but elongates weakly whereas DIA1 has potent elongation activity but does not sever. Using cryo-electron microscopy (cryo-EM) we show five structural states of INF2 and two of DIA1 bound to the middle and barbed end of F-actin. INF2 and DIA1 bind differently to these sites, consistent with their distinct activities. The formin-homology 2 and Wiskott-Aldrich syndrome protein-homology 2 (FH2 and WH2, respectively) domains of INF2 are positioned to sever F-actin, whereas DIA1 appears unsuited for severing. These structures also show how profilin-actin is delivered to the fast-growing barbed end, and how this is followed by a transition of the incoming monomer into the F-actin conformation and the release of profilin. Combined, the seven structures presented here provide step-by-step visualization of the mechanisms of F-actin severing and elongation by formins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44135.map.gz | 32.2 MB | EMDB map data format | |
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Header (meta data) | emd-44135-v30.xml emd-44135.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44135_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_44135.png | 34.1 KB | ||
Masks | emd_44135_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-44135.cif.gz | 6.8 KB | ||
Others | emd_44135_half_map_1.map.gz emd_44135_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44135 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44135 | HTTPS FTP |
-Validation report
Summary document | emd_44135_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_44135_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_44135_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_44135_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44135 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44135 | HTTPS FTP |
-Related structure data
Related structure data | 9b3dMC 9az4C 9azpC 9azqC 9b03C 9b0kC 9b27C M: atomic model generated by this map C: citing same article (ref.) |
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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_44135.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_44135_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_44135_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_44135_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of mDia1 dimer bound at the barbed end of actin filaments.
Entire | Name: Structure of mDia1 dimer bound at the barbed end of actin filaments. |
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Components |
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-Supramolecule #1: Structure of mDia1 dimer bound at the barbed end of actin filaments.
Supramolecule | Name: Structure of mDia1 dimer bound at the barbed end of actin filaments. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 252 KDa |
-Supramolecule #2: mDia1 dimer
Supramolecule | Name: mDia1 dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #3: Actin filament
Supramolecule | Name: Actin filament / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 41.387227 KDa |
Sequence | String: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP ...String: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSY E LPDGQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVMSG GTTMYPGIAD RMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKCF UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #2: Protein diaphanous homolog 1
Macromolecule | Name: Protein diaphanous homolog 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 46.313004 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VLPFGLTPKK VYKPEVQLRR PNWSKFVAED LSQDCFWTKV KEDRFENNEL FAKLTLAFSA QTKTSKAKKD QEGGEEKKSV QKKKVKELK VLDSKTAQNL SIFLGSFRMP YQEIKNVILE VNEAVLTESM IQNLIKQMPE PEQLKMLSEL KEEYDDLAES E QFGVVMGT ...String: VLPFGLTPKK VYKPEVQLRR PNWSKFVAED LSQDCFWTKV KEDRFENNEL FAKLTLAFSA QTKTSKAKKD QEGGEEKKSV QKKKVKELK VLDSKTAQNL SIFLGSFRMP YQEIKNVILE VNEAVLTESM IQNLIKQMPE PEQLKMLSEL KEEYDDLAES E QFGVVMGT VPRLRPRLNA ILFKLQFSEQ VENIKPEIVS VTAACEELRK SENFSSLLEL TLLVGNYMNA GSRNAGAFGF NI SFLCKLR DTKSADQKMT LLHFLAELCE NDHPEVLKFP DELAHVEKAS RVSAENLQKS LDQMKKQIAD VERDVQNFPA ATD EKDKFV EKMTSFVKDA QEQYNKLRMM HSNMETLYKE LGDYFVFDPK KLSVEEFFMD LHNFRNMFLQ AVKENQKRRE TEE UniProtKB: Protein diaphanous homolog 1 |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / 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: 6 / 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
Concentration | 1.48 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: 20mM HEPES, 50mM NaCL, 1mM EDTA, 1mM DTT, 0.05% Thesit | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Actin filaments were sonicated prior to addition of mDia1 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |