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Yorodumi- EMDB-13061: Tomogram of nuclear envelope of MEF cell carrying homozygous H222... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13061 | |||||||||
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Title | Tomogram of nuclear envelope of MEF cell carrying homozygous H222P mutation in Lmna. | |||||||||
Map data | Tomogram of nuclear envelope of MEF carrying LmnaH222P/H222P mutation. | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Kronenberg-Tenga R | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: J Cell Sci / Year: 2021 Title: A lamin A/C variant causing striated muscle disease provides insights into filament organization. Authors: Rafael Kronenberg-Tenga / Meltem Tatli / Matthias Eibauer / Wei Wu / Ji-Yeon Shin / Gisèle Bonne / Howard J Worman / Ohad Medalia / Abstract: The gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in cause a wide ...The gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in cause a wide variety of pathologies. In this study, we analyzed the nuclear lamina of embryonic fibroblasts from mice, which develop cardiomyopathy and muscular dystrophy. Although the organization of the lamina appeared unaltered, there were changes in chromatin and B-type lamin expression. An increase in nuclear size and consequently a relative reduction in heterochromatin near the lamina allowed for a higher resolution structural analysis of lamin filaments using cryo-electron tomography. This was most apparent when visualizing lamin filaments and using a nuclear extraction protocol. Averaging of individual segments of filaments in mouse fibroblasts resolved two polymers that constitute the mature filaments. Our findings provide better views of the organization of lamin filaments and the effect of a striated muscle disease-causing mutation on nuclear structure. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13061.map.gz | 606.8 MB | EMDB map data format | |
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Header (meta data) | emd-13061-v30.xml emd-13061.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_13061.png | 267.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13061 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13061 | HTTPS FTP |
-Validation report
Summary document | emd_13061_validation.pdf.gz | 355.5 KB | Display | EMDB validaton report |
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Full document | emd_13061_full_validation.pdf.gz | 355 KB | Display | |
Data in XML | emd_13061_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_13061_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13061 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13061 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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EM raw data | EMPIAR-10601 (Title: A lamin A/C variant causing striated muscle disease provides insights into filament organization Data size: 2.7 Data #1: Tilt-series of LmnaH222P/H222P revealing lamin meshwork in nuclease treated and FIB-milled nucleus [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13061.map.gz / Format: CCP4 / Size: 662.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Tomogram of nuclear envelope of MEF carrying LmnaH222P/H222P mutation. | ||||||||||||||||||||
Voxel size | X=Y=Z: 8.82603 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : H222P MEF
Entire | Name: H222P MEF |
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Components |
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-Supramolecule #1: H222P MEF
Supramolecule | Name: H222P MEF / type: cell / ID: 1 / Parent: 0 Details: MEF cell carrying homozygous H222P mutation in Lmna. |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD |
Vitrification | Cryogen name: ETHANE |
Details | MEF cell carrying homozygous H222P mutation in Lmna. |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.24 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 128 K / Focused ion beam - Initial thickness: 4000 nm / Focused ion beam - Final thickness: 200 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Zeiss Auriga. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD / Number images used: 41 |
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