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Yorodumi- EMDB-42918: Cryo-EM Structure of Wildtype Smooth Muscle Gamma Actin (ACTG2) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42918 | |||||||||
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Title | Cryo-EM Structure of Wildtype Smooth Muscle Gamma Actin (ACTG2) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Filament / Actin / Smooth Muscle / CYTOSOLIC PROTEIN / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information myosin filament / mesenchyme migration / Smooth Muscle Contraction / filopodium / cell periphery / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / blood microparticle / cytoskeleton ...myosin filament / mesenchyme migration / Smooth Muscle Contraction / filopodium / cell periphery / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / blood microparticle / cytoskeleton / hydrolase activity / positive regulation of gene expression / extracellular space / extracellular exosome / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.45 Å | |||||||||
Authors | Palmer NJ / Carman PJ / Ceron RH / Dominguez R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Molecular mechanisms linking missense ACTG2 mutations to visceral myopathy. Authors: Rachel H Ceron / Faviolla A Báez-Cruz / Nicholas J Palmer / Peter J Carman / Malgorzata Boczkowska / Robert O Heuckeroth / E Michael Ostap / Roberto Dominguez / Abstract: Visceral myopathy is a life-threatening disease characterized by muscle weakness in the bowel, bladder, and uterus. Mutations in smooth muscle γ-actin (ACTG2) are the most common cause of the ...Visceral myopathy is a life-threatening disease characterized by muscle weakness in the bowel, bladder, and uterus. Mutations in smooth muscle γ-actin (ACTG2) are the most common cause of the disease, but the mechanisms by which the mutations alter muscle function are unknown. Here, we examined four prevalent ACTG2 mutations (R40C, R148C, R178C, and R257C) that cause different disease severity and are spread throughout the actin fold. R178C displayed premature degradation, R148C disrupted interactions with actin-binding proteins, R40C inhibited polymerization, and R257C destabilized filaments. Because these mutations are heterozygous, we also analyzed 50/50 mixtures with wild-type (WT) ACTG2. The WT/R40C mixture impaired filament nucleation by leiomodin 1, and WT/R257C produced filaments that were easily fragmented by smooth muscle myosin. Smooth muscle tropomyosin isoform Tpm1.4 partially rescued the defects of R40C and R257C. Cryo-electron microscopy structures of filaments formed by R40C and R257C revealed disrupted intersubunit contacts. The biochemical and structural properties of the mutants correlate with their genotype-specific disease severity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42918.map.gz | 32.5 MB | EMDB map data format | |
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Header (meta data) | emd-42918-v30.xml emd-42918.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42918_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_42918.png | 71.2 KB | ||
Masks | emd_42918_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-42918.cif.gz | 6.5 KB | ||
Others | emd_42918_half_map_1.map.gz emd_42918_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42918 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42918 | HTTPS FTP |
-Validation report
Summary document | emd_42918_validation.pdf.gz | 940.5 KB | Display | EMDB validaton report |
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Full document | emd_42918_full_validation.pdf.gz | 940 KB | Display | |
Data in XML | emd_42918_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_42918_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42918 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42918 | HTTPS FTP |
-Related structure data
Related structure data | 8v2oMC 8v30C 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_42918.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_42918_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42918_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42918_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ACTG2 filament
Entire | Name: ACTG2 filament |
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Components |
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-Supramolecule #1: ACTG2 filament
Supramolecule | Name: ACTG2 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: ACTG2 filaments, purified from Expi293 cells |
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Source (natural) | Organism: Homo sapiens (human) / Tissue: Smooth |
-Macromolecule #1: Actin, gamma-enteric smooth muscle
Macromolecule | Name: Actin, gamma-enteric smooth muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / 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: Homo sapiens (human) / Tissue: Smooth Muscle |
Molecular weight | Theoretical: 41.935816 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MCEEETTALV CDNGSGLCKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GI ITN WDDMEKIWHH SFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDS GD GVTHNVPIYE ...String: MCEEETTALV CDNGSGLCKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GI ITN WDDMEKIWHH SFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDS GD GVTHNVPIYE GYALPHAIMR LDLAGRDLTD YLMKILTERG YSFVTTAERE IVRDIKEKLC YVALDFENEM ATAASSSS L EKSYELPDGQ VITIGNERFR CPETLFQPSF IGMESAGIHE TTYNSIMKCD IDIRKDLYAN NVLSGGTTMY PGIADRMQK EITALAPSTM KIKIIAPPER KYSVWIGGSI LASLSTFQQM WISKPEYDEA GPSIVHRKCF UniProtKB: Actin, gamma-enteric smooth muscle |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.168 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
Details: Actin F-buffer | |||||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: Blot Force: 0 Blot Time: 2.5 s. | |||||||||||||||||||||
Details | ACTG2 F-Actin in the ADP state. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 526 / Average electron dose: 45.0 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 / 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 |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8v2o: |