+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17120 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM map of zebrafish cardiac F-actin | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | F-actin / Actin / Cardiac Actin / Filamentous / CONTRACTILE PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Bradshaw M / Squire JM / Morris E / Atkinson G / Richardson B / Lees J / Paul DM | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
Citation | Journal: J Muscle Res Cell Motil / Year: 2023 Title: Zebrafish as a model for cardiac disease; Cryo-EM structure of native cardiac thin filaments from Danio Rerio. Authors: Marston Bradshaw / John M Squire / Edward Morris / Georgia Atkinson / Rebecca Richardson / Jon Lees / Massimo Caputo / Giulia M Bigotti / Danielle M Paul / Abstract: Actin, tropomyosin and troponin, the proteins that comprise the contractile apparatus of the cardiac thin filament, are highly conserved across species. We have used cryo-EM to study the three- ...Actin, tropomyosin and troponin, the proteins that comprise the contractile apparatus of the cardiac thin filament, are highly conserved across species. We have used cryo-EM to study the three-dimensional structure of the zebrafish cardiac thin and actin filaments. With 70% of human genes having an obvious zebrafish orthologue, and conservation of 85% of disease-causing genes, zebrafish are a good animal model for the study of human disease. Our structure of the zebrafish thin filament reveals the molecular interactions between the constituent proteins, showing that the fundamental organisation of the complex is the same as that reported in the human reconstituted thin filament. A reconstruction of zebrafish cardiac F-actin demonstrates no deviations from human cardiac actin over an extended length of 14 actin subunits. Modelling zebrafish homology models into our maps enabled us to compare, in detail, the similarity with human models. The structural similarities of troponin-T in particular, a region known to contain a hypertrophic cardiomyopathy 'hotspot', confirm the suitability of zebrafish to study these disease-causing mutations. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_17120.map.gz | 448 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-17120-v30.xml emd-17120.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17120_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_17120.png | 53.6 KB | ||
Masks | emd_17120_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-17120.cif.gz | 6.1 KB | ||
Others | emd_17120_half_map_1.map.gz emd_17120_half_map_2.map.gz | 168.8 MB 168.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17120 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17120 | HTTPS FTP |
-Validation report
Summary document | emd_17120_validation.pdf.gz | 955.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_17120_full_validation.pdf.gz | 955.1 KB | Display | |
Data in XML | emd_17120_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | emd_17120_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17120 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17120 | HTTPS FTP |
-Related structure data
Related structure data | 8ordMC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_17120.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_17120_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_17120_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_17120_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Cardiac F-actin
Entire | Name: Cardiac F-actin |
---|---|
Components |
|
-Supramolecule #1: Cardiac F-actin
Supramolecule | Name: Cardiac F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Danio rerio (zebrafish) / Organ: Heart / Tissue: Ventrical / Location in cell: Sarcomere |
-Macromolecule #1: Actin, alpha 1b, skeletal muscle
Macromolecule | Name: Actin, alpha 1b, skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Danio rerio (zebrafish) / Organ: Heart / Tissue: Ventrical |
Molecular weight | Theoretical: 42.021887 KDa |
Sequence | String: MCDEEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPVLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDAGD G VTHNVPVY ...String: MCDEEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPVLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDAGD G VTHNVPVY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNGIMKC DIDIRKDLYA NNVLSGGTTM YPGIGDRMQK EIT ALAPST MKIKMIAPPE RKYSVWIGGS ILASLSTFQQ MWISKDEYEE AGPSIVHRKC F UniProtKB: Actin, alpha 1b, skeletal muscle |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #3: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: PO4 |
---|---|
Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.8 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 6.8 Component:
Details: Phosphate Buffer Protease Inhibitor Cocktail (0.44 mg/ml) | ||||||||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa / Details: 15 mAh | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP | ||||||||||||||||||
Details | Freshly excised heart tissue from Zebrafish. Monodispersed filaments of varying lengths. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-35 / Number grids imaged: 2 / Number real images: 5622 / Average electron dose: 38.85 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 1.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.4 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 |