+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17737 | |||||||||
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Title | ATTRG47E amyloid fibril from hereditary ATTR amloidosis | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transthyretin / ATTR amyloidosis / ATTRG47E / amyloid fibril / misfolding disease / cryo-EM / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.3673 Å | |||||||||
Authors | Steinebrei M / Schmidt M / Faendrich M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Common transthyretin-derived amyloid fibril structures in patients with hereditary ATTR amyloidosis. Authors: Maximilian Steinebrei / Julian Baur / Anaviggha Pradhan / Niklas Kupfer / Sebastian Wiese / Ute Hegenbart / Stefan O Schönland / Matthias Schmidt / Marcus Fändrich / Abstract: Systemic ATTR amyloidosis is an increasingly important protein misfolding disease that is provoked by the formation of amyloid fibrils from transthyretin protein. The pathological and clinical ...Systemic ATTR amyloidosis is an increasingly important protein misfolding disease that is provoked by the formation of amyloid fibrils from transthyretin protein. The pathological and clinical disease manifestations and the number of pathogenic mutational changes in transthyretin are highly diverse, raising the question whether the different mutations may lead to different fibril morphologies. Using cryo-electron microscopy, however, we show here that the fibril structure is remarkably similar in patients that are affected by different mutations. Our data suggest that the circumstances under which these fibrils are formed and deposited inside the body - and not only the fibril morphology - are crucial for defining the phenotypic variability in many patients. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17737.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-17737-v30.xml emd-17737.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17737_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_17737.png | 90.7 KB | ||
Filedesc metadata | emd-17737.cif.gz | 5.2 KB | ||
Others | emd_17737_half_map_1.map.gz emd_17737_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17737 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17737 | HTTPS FTP |
-Validation report
Summary document | emd_17737_validation.pdf.gz | 686.5 KB | Display | EMDB validaton report |
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Full document | emd_17737_full_validation.pdf.gz | 686.1 KB | Display | |
Data in XML | emd_17737_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_17737_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17737 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17737 | HTTPS FTP |
-Related structure data
Related structure data | 8pkfMC 8pkeC 8pkgC 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_17737.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: 0.934 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_17737_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17737_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ATTRG47E amyloid fibril
Entire | Name: ATTRG47E amyloid fibril |
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Components |
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-Supramolecule #1: ATTRG47E amyloid fibril
Supramolecule | Name: ATTRG47E amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: amyloid fibril of Transthyretin with G47E mutation in hereditary ATTR amyloidosis |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Heart / Tissue: Heart muscle |
-Macromolecule #1: Transthyretin
Macromolecule | Name: Transthyretin / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Heart |
Molecular weight | Theoretical: 13.849423 KDa |
Sequence | String: GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASEKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPFHE HAEVVFTAND SGPRRYTIAA LLSPYSYSTT AVVTNPKE UniProtKB: Transthyretin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 / Details: Water |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP |
Details | amyloid fibril of Transthyretin with G47E mutation |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 12067 / Average exposure time: 9.0 sec. / Average electron dose: 41.63 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |