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Yorodumi- PDB-7ob4: Cryo-EM structure of a twisted-dimer transthyretin amyloid fibril... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ob4 | ||||||
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Title | Cryo-EM structure of a twisted-dimer transthyretin amyloid fibril from vitreous body of the eye | ||||||
Components | Transthyretin | ||||||
Keywords | PROTEIN FIBRIL / AMYLOID FIBRIL / TRANSTHYRETIN / MISFOLDING / ATTR AMYLOIDOSIS / V30M VARIANT / EX VIVO / VITREOUS BODY | ||||||
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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.22 Å | ||||||
Authors | Iakovleva, I. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for transthyretin amyloid formation in vitreous body of the eye. Authors: Irina Iakovleva / Michael Hall / Melanie Oelker / Linda Sandblad / Intissar Anan / A Elisabeth Sauer-Eriksson / Abstract: Amyloid transthyretin (ATTR) amyloidosis is characterized by the abnormal accumulation of ATTR fibrils in multiple organs. However, the structure of ATTR fibrils from the eye is poorly understood. ...Amyloid transthyretin (ATTR) amyloidosis is characterized by the abnormal accumulation of ATTR fibrils in multiple organs. However, the structure of ATTR fibrils from the eye is poorly understood. Here, we used cryo-EM to structurally characterize vitreous body ATTR fibrils. These structures were distinct from previously characterized heart fibrils, even though both have the same mutation and type A pathology. Differences were observed at several structural levels: in both the number and arrangement of protofilaments, and the conformation of the protein fibril in each layer of protofilaments. Thus, our results show that ATTR protein structure and its assembly into protofilaments in the type A fibrils can vary between patients carrying the same mutation. By analyzing and matching the interfaces between the amino acids in the ATTR fibril with those in the natively folded TTR, we are able to propose a mechanism for the structural conversion of TTR into a fibrillar form. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ob4.cif.gz | 226.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ob4.ent.gz | 182.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ob4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ob4_validation.pdf.gz | 967.7 KB | Display | wwPDB validaton report |
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Full document | 7ob4_full_validation.pdf.gz | 1003.3 KB | Display | |
Data in XML | 7ob4_validation.xml.gz | 42.6 KB | Display | |
Data in CIF | 7ob4_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/7ob4 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/7ob4 | HTTPS FTP |
-Related structure data
Related structure data | 12794MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 13809.426 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Transthyretin derived amyloid fibril (V30M) from vitreous body Type: TISSUE / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Vitreous body of the eye |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 28.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -0.552 ° / Axial rise/subunit: 4.72 Å / Axial symmetry: C2 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 130212 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27778 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6SDZ Accession code: 6SDZ / Source name: PDB / Type: experimental model |