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Yorodumi- EMDB-19522: Structure of the formin INF2 bound to the barbed end of F-actin. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19522 | ||||||||||||
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Title | Structure of the formin INF2 bound to the barbed end of F-actin. | ||||||||||||
Map data | Sharpened, local-resolution filtered cryo-EM density map of the formin INF2 bound to the barbed end of actin filaments. | ||||||||||||
Sample |
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Keywords | actin / formin / INF2 / actin end / barbed end / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / regulation of mitochondrial fission / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / regulation of mitochondrial fission / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / small GTPase binding / calcium-dependent protein binding / lamellipodium / actin binding / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 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_19522.map.gz | 106.3 MB | EMDB map data format | |
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Header (meta data) | emd-19522-v30.xml emd-19522.xml | 40.2 KB 40.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19522_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_19522.png | 94.8 KB | ||
Masks | emd_19522_msk_1.map emd_19522_msk_2.map | 178 MB 178 MB | Mask map | |
Filedesc metadata | emd-19522.cif.gz | 8.9 KB | ||
Others | emd_19522_additional_1.map.gz emd_19522_additional_2.map.gz emd_19522_additional_3.map.gz emd_19522_additional_4.map.gz emd_19522_additional_5.map.gz emd_19522_additional_6.map.gz emd_19522_half_map_1.map.gz emd_19522_half_map_2.map.gz | 88.9 MB 165.3 MB 165.3 MB 140.4 MB 168.2 MB 105.4 MB 141.2 MB 141.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19522 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19522 | HTTPS FTP |
-Validation report
Summary document | emd_19522_validation.pdf.gz | 829.3 KB | Display | EMDB validaton report |
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Full document | emd_19522_full_validation.pdf.gz | 828.9 KB | Display | |
Data in XML | emd_19522_validation.xml.gz | 20 KB | Display | |
Data in CIF | emd_19522_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19522 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19522 | HTTPS FTP |
-Related structure data
Related structure data | 8rv2MC 8rttC 8rtyC 8ru0C 8ru2C 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_19522.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened, local-resolution filtered cryo-EM density map of the formin INF2 bound to the barbed end of actin filaments. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.9 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Mask #1
+Mask #2
+Additional map: 3D-refined, unsharpened cryo-EM density map of INF2 bound...
+Additional map: Unfiltered half map 1 of the formin INF2...
+Additional map: Unfiltered half map 2 of the formin INF2...
+Additional map: 3D-refined, unsharpened cryo-EM density map of the formin...
+Additional map: Sharpened cryo-EM density map of the formin INF2...
+Additional map: Composite map computed with the main map of...
+Half map: Unfiltered half map 1 of the formin INF2...
+Half map: Unfiltered half map 2 of the formin INF2...
-Sample components
-Entire : Complex of the formin INF2 dimer that binds to the actin subunits...
Entire | Name: Complex of the formin INF2 dimer that binds to the actin subunits at the barbed end of actin filaments. |
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Components |
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-Supramolecule #1: Complex of the formin INF2 dimer that binds to the actin subunits...
Supramolecule | Name: Complex of the formin INF2 dimer that binds to the actin subunits at the barbed end of actin filaments. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Alpha actin was purified from rabbit skeletal muscle. INF2 was purified from E. coli. Actin filaments were co-polymerized in the presence of the formin INF2 prior to cryo-EM grid preparation. |
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-Supramolecule #2: Actin filament barbed end
Supramolecule | Name: Actin filament barbed end / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: Complex of the actin subunits that form the barbed end of actin filaments. |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle |
-Supramolecule #3: INF2 dimer
Supramolecule | Name: INF2 dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 Details: This dimer is composed of the FH2 domain of the formin INF2. |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 Details: Rabbit skeletal alpha actin purified from frozen rabbit muscle acetone powder. Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle |
Molecular weight | Theoretical: 41.875633 KDa |
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: Isoform 2 of Inverted formin-2
Macromolecule | Name: Isoform 2 of Inverted formin-2 / type: protein_or_peptide / ID: 2 Details: INF2 FH1FH2C nonCAAX isoform was recombinantly expressed in E. coli BL21 Star pRARE cells and purified. This compound consists of the formin homology 1 and 2 domains, as well as the C- ...Details: INF2 FH1FH2C nonCAAX isoform was recombinantly expressed in E. coli BL21 Star pRARE cells and purified. This compound consists of the formin homology 1 and 2 domains, as well as the C-terminal region of the human formin INF2 isoform nonCAAX. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 84.453711 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GGGGGMAPPA PPLPPPLPGS CEFLSPPPPP LPGLGCPPPP PPLLPGMGWG PPPPPPPLLP CTCSPPVAGG MEEVIVAQVD HGLGSAWVP SHRRVNPPTL RMKKLNWQKL PSNVAREHNS MWASLSSPDA EAVEPDFSSI ERLFSFPAAK PKEPTMVAPR A RKEPKEIT ...String: GGGGGMAPPA PPLPPPLPGS CEFLSPPPPP LPGLGCPPPP PPLLPGMGWG PPPPPPPLLP CTCSPPVAGG MEEVIVAQVD HGLGSAWVP SHRRVNPPTL RMKKLNWQKL PSNVAREHNS MWASLSSPDA EAVEPDFSSI ERLFSFPAAK PKEPTMVAPR A RKEPKEIT FLDAKKSLNL NIFLKQFKCS NEEVAAMIRA GDTTKFDVEV LKQLLKLLPE KHEIENLRAF TEERAKLASA DH FYLLLLA IPCYQLRIEC MLLCEGAAAV LDMVRPKAQL VLAACESLLT SRQLPIFCQL ILRIGNFLNY GSHTGDADGF KIS TLLKLT ETKSQQNRVT LLHHVLEEAE KSHPDLLQLP RDLEQPSQAA GINLEIIRSE ASSNLKKLLE TERKVSASVA EVQE QYTER LQASISAFRA LDELFEAIEQ KQRELADYLC EDAQQLSLED TFSTMKAFRD LFLRALKENK DRKEQAAKAE RRKQQ LAEE EARRPRGEDG KPVRKGPGKQ EEVCVIDALL ADIRKGFQLR KTARGRGDTD GGSKAASMDP PRATEPVATS NPAGDP VGS TRCPASEPGL DATTASESRG WDLVDAVTPG PQPTLEQLEE GGPRPLERRS SWYVDASDVL TTEDPQCPQP LEGAWPV TL GDAQALKPLK FSSNQPPAAG SSRQDAKDPT SLLGVLQAEA DSTSEGLEDA VHSRGARPPA AGPGGDEDED EEDTAPES A LDTSLDKSFS EDAVTDSSGS GTLPRARGRA SKGTGKRRKK RPSRSQEGLR PRPKAK UniProtKB: Inverted formin-2 |
-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: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-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:
Details: 12 mM HEPES pH 7.1, 100 mM KCl, 2.1 mM MgCl2, 1 mM EGTA, 1 mM TCEP, 0.2 mM ATP | |||||||||||||||||||||
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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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Specialist optics | Spherical aberration corrector: 300 kV Titan Krios G3 microscope (Thermo Fisher Scientific). Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV / Details: Gatan energy filter. |
Details | 300 kV Titan Krios G3 microscope (Thermo Fisher Scientific). |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 20305 / Average electron dose: 60.6 e/Å2 |
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | Real Space Refinement in Phenix. | |||||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT | |||||||||
Output model | PDB-8rv2: |