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Yorodumi- PDB-6zcf: Amyloid fibril morphology i (in vitro) from murine SAA1.1 protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zcf | |||||||||||||||||||||
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Title | Amyloid fibril morphology i (in vitro) from murine SAA1.1 protein | |||||||||||||||||||||
Components | Serum amyloid A-2 protein | |||||||||||||||||||||
Keywords | PROTEIN FIBRIL / systemic amyloidosis / misfolding disease / inflammation / prion | |||||||||||||||||||||
Function / homology | Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins / response to stilbenoid / high-density lipoprotein particle / acute-phase response / Serum amyloid A-2 protein Function and homology information | |||||||||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.73 Å | |||||||||||||||||||||
Authors | Bansal, A. / Schmidt, M. / Faendrich, M. | |||||||||||||||||||||
Funding support | Germany, 6items
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Citation | Journal: Nat Commun / Year: 2021 Title: AA amyloid fibrils from diseased tissue are structurally different from in vitro formed SAA fibrils. Authors: Akanksha Bansal / Matthias Schmidt / Matthies Rennegarbe / Christian Haupt / Falk Liberta / Sabrina Stecher / Ioana Puscalau-Girtu / Alexander Biedermann / Marcus Fändrich / Abstract: Systemic AA amyloidosis is a world-wide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from serum amyloid A (SAA) protein. Using cryo ...Systemic AA amyloidosis is a world-wide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from serum amyloid A (SAA) protein. Using cryo electron microscopy we here show that amyloid fibrils which were purified from AA amyloidotic mice are structurally different from fibrils formed from recombinant SAA protein in vitro. Ex vivo amyloid fibrils consist of fibril proteins that contain more residues within their ordered parts and possess a higher β-sheet content than in vitro fibril proteins. They are also more resistant to proteolysis than their in vitro formed counterparts. These data suggest that pathogenic amyloid fibrils may originate from proteolytic selection, allowing specific fibril morphologies to proliferate and to cause damage to the surrounding tissue. | |||||||||||||||||||||
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 | 6zcf.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zcf.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zcf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6zcf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6zcf_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 6zcf_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/6zcf ftp://data.pdbj.org/pub/pdb/validation_reports/zc/6zcf | HTTPS FTP |
-Related structure data
Related structure data | 11162MC 6zcgC 6zchC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-11027 (Title: Cryo electron microscopy of in vitro recombinant SAA1.1 amyloid fibrils Data size: 525.4 Data #1: Unaligned multiframe micrographs of ex-vivo murine SAA1 [micrographs - multiframe] Data #2: Thumbnails for micrographs of ex-vivo murine SAA1 [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 11622.629 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Saa2 / Production host: Escherichia coli (E. coli) / References: UniProt: P05367 |
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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: Serum amyloid A1 (SAA1) amyloid fibril / Type: COMPLEX / Details: in vitro murine SAA amyloid fibril morphology i / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8.5 / Details: 10mM Tris(hydroxymethyl)aminomethane (Tris) |
Buffer component | Conc.: 10 mM / Name: Tris(hydroxymethyl)aminomethane / Formula: (HOCH2)3CNH2 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 96 % |
-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 / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 12 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 178.93 ° / Axial rise/subunit: 2.3719 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 94220 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93347 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient |