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Yorodumi- EMDB-10150: transthyritin derived amyloid fibril from patient with hereditary... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10150 | |||||||||
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Title | transthyritin derived amyloid fibril from patient with hereditary V30M ATTR amyloidosis | |||||||||
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Sample |
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Keywords | amyloid fibril / systemic ATTR amyloidosis / ex vivo / misfolding / patient tissue / transthyritin / 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: 2.97 Å | |||||||||
Authors | Schmidt M / Faendrich M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis. Authors: Matthias Schmidt / Sebastian Wiese / Volkan Adak / Jonas Engler / Shubhangi Agarwal / Günter Fritz / Per Westermark / Martin Zacharias / Marcus Fändrich / Abstract: ATTR amyloidosis is one of the worldwide most abundant forms of systemic amyloidosis. The disease is caused by the misfolding of transthyretin protein and the formation of amyloid deposits at ...ATTR amyloidosis is one of the worldwide most abundant forms of systemic amyloidosis. The disease is caused by the misfolding of transthyretin protein and the formation of amyloid deposits at different sites within the body. Here, we present a 2.97 Å cryo electron microscopy structure of a fibril purified from the tissue of a patient with hereditary Val30Met ATTR amyloidosis. The fibril consists of a single protofilament that is formed from an N-terminal and a C-terminal fragment of transthyretin. Our structure provides insights into the mechanism of misfolding and implies the formation of an early fibril state from unfolded transthyretin molecules, which upon proteolysis converts into mature ATTR amyloid fibrils. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10150.map.gz | 952.2 KB | EMDB map data format | |
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Header (meta data) | emd-10150-v30.xml emd-10150.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10150_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_10150.png | 59 KB | ||
Filedesc metadata | emd-10150.cif.gz | 5.3 KB | ||
Others | emd_10150_half_map_1.map.gz emd_10150_half_map_2.map.gz | 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10150 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10150 | HTTPS FTP |
-Validation report
Summary document | emd_10150_validation.pdf.gz | 647 KB | Display | EMDB validaton report |
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Full document | emd_10150_full_validation.pdf.gz | 646.6 KB | Display | |
Data in XML | emd_10150_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_10150_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10150 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10150 | HTTPS FTP |
-Related structure data
Related structure data | 6sdzMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10150.map.gz / Format: CCP4 / Size: 30.5 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:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_10150_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10150_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Transthyretin derived amyloid fibril (V30M)
Entire | Name: Transthyretin derived amyloid fibril (V30M) |
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Components |
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-Supramolecule #1: Transthyretin derived amyloid fibril (V30M)
Supramolecule | Name: Transthyretin derived amyloid fibril (V30M) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: ex vivo ATTR amyloid fibril from human tissue |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transthyretin
Macromolecule | Name: Transthyretin / type: protein_or_peptide / ID: 1 Details: transthyritin V30M fragments, residues 11-35 and residues 57-123 Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.809426 KDa |
Sequence | String: GPTGTGESKC PLMVKVLDAV RGSPAINVAM HVFRKAADDT WEPFASGKTS 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 extract |
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 96 % / Instrument: FEI VITROBOT MARK III |
-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: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 89.59 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-6sdz: |