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- PDB-8e7j: Cryo-EM structure of cardiac amyloid fibril from a variant ATTR I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e7j | |||||||||
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Title | Cryo-EM structure of cardiac amyloid fibril from a variant ATTR I84S amyloidosis patient | |||||||||
![]() | Transthyretin | |||||||||
![]() | PROTEIN FIBRIL / Transthyretin / Amyloidosis / Systemic amyloidosis / ATTR / Cardiac | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Nguyen, B.A. / Saelices, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy. Authors: Binh An Nguyen / Virender Singh / Shumaila Afrin / Anna Yakubovska / Lanie Wang / Yasmin Ahmed / Rose Pedretti / Maria Del Carmen Fernandez-Ramirez / Preeti Singh / Maja Pękała / Luis O ...Authors: Binh An Nguyen / Virender Singh / Shumaila Afrin / Anna Yakubovska / Lanie Wang / Yasmin Ahmed / Rose Pedretti / Maria Del Carmen Fernandez-Ramirez / Preeti Singh / Maja Pękała / Luis O Cabrera Hernandez / Siddharth Kumar / Andrew Lemoff / Roman Gonzalez-Prieto / Michael R Sawaya / David S Eisenberg / Merrill Douglas Benson / Lorena Saelices / ![]() ![]() Abstract: ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic ...ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. In brain amyloid conditions, previous studies suggest an association between clinical phenotype and the molecular structures of their amyloid fibrils. Here we investigate whether there is such an association in ATTRv amyloidosis patients carrying the mutation I84S. Using cryo-electron microscopy, we determined the structures of cardiac fibrils extracted from three ATTR amyloidosis patients carrying the ATTRv-I84S mutation, associated with a consistent clinical phenotype. We found that in each ATTRv-I84S patient, the cardiac fibrils exhibited different local conformations, and these variations can co-exist within the same fibril. Our finding suggests that one amyloid disease may associate with multiple fibril structures in systemic amyloidoses, calling for further studies. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.3 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27323MC ![]() 8e7eC ![]() 8tdnC ![]() 8tdoC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 15878.902 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Cardiac amyloid fibril of variant ATTR I84S amyloidosis Type: TISSUE / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -1.25 ° / Axial rise/subunit: 4.76 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98953 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE | ||||||||||||||||||||||||||||
Refine LS restraints |
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