+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15361 | ||||||||||||
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Title | Wild type ATTR amyloid fibril from senile systemic amyloidosis | ||||||||||||
Map data | |||||||||||||
Sample |
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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) / human (human) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.78 Å | ||||||||||||
Authors | Schmidt M / Steinebrei M | ||||||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structure of an ATTRwt amyloid fibril from systemic non-hereditary transthyretin amyloidosis. Authors: Maximilian Steinebrei / Juliane Gottwald / Julian Baur / Christoph Röcken / Ute Hegenbart / Stefan Schönland / Matthias Schmidt / Abstract: Wild type transthyretin-derived amyloid (ATTRwt) is the major component of non-hereditary transthyretin amyloidosis. Its accumulation in the heart of elderly patients is life threatening. A variety ...Wild type transthyretin-derived amyloid (ATTRwt) is the major component of non-hereditary transthyretin amyloidosis. Its accumulation in the heart of elderly patients is life threatening. A variety of genetic variants of transthyretin can lead to hereditary transthyretin amyloidosis, which shows different clinical symptoms, like age of onset and pattern of organ involvement. However, in the case of non-hereditary transthyretin amyloidosis ATTRwt fibril deposits are located primarily in heart tissue. In this structural study we analyzed ATTRwt amyloid fibrils from the heart of a patient with non-hereditary transthyretin amyloidosis. We present a 2.78 Å reconstructed density map of these ATTRwt fibrils using cryo electron microscopy and compare it with previously published V30M variants of ATTR fibrils extracted from heart and eye of different patients. All structures show a remarkably similar spearhead like shape in their cross section, formed by the same N- and C-terminal fragments of transthyretin with some minor differences. This demonstrates common features for ATTR fibrils despite differences in mutations and patients. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15361.map.gz | 495.2 KB | EMDB map data format | |
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Header (meta data) | emd-15361-v30.xml emd-15361.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15361_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_15361.png | 8.3 MB | ||
Others | emd_15361_half_map_1.map.gz emd_15361_half_map_2.map.gz | 80.6 MB 80.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15361 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15361 | HTTPS FTP |
-Validation report
Summary document | emd_15361_validation.pdf.gz | 567.6 KB | Display | EMDB validaton report |
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Full document | emd_15361_full_validation.pdf.gz | 567.2 KB | Display | |
Data in XML | emd_15361_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_15361_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15361 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15361 | HTTPS FTP |
-Related structure data
Related structure data | 8adeMC 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_15361.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15361_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15361_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Transthyretin amyolid fibrils
Entire | Name: Transthyretin amyolid fibrils |
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Components |
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-Supramolecule #1: Transthyretin amyolid fibrils
Supramolecule | Name: Transthyretin amyolid fibrils / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: human (human) |
Molecular weight | Theoretical: 13.77736 KDa |
Sequence | String: GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPFHE HAEVVFTAND SGPRRYTIAA LLSPYSYSTT AVVTNPKE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295.1500 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |