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Yorodumi- PDB-8qut: Cryo-EM structure of the heat-irreversible amyloid fibrils of hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qut | ||||||
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Title | Cryo-EM structure of the heat-irreversible amyloid fibrils of human lysozyme | ||||||
Components |
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Keywords | PROTEIN FIBRIL / amyloid / irreversible | ||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / 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: 2.8 Å | ||||||
Authors | Frey, L. / Greenwald, J. / Riek, R. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To be published Title: Structural insights into reversible versus irreversible amyloid fibril formation from a single protein Authors: Frey, L. / Zhou, J. / Cereghetti, G. / Emanuel, M. / Greenwald, J. / Rhyner, D. / Pokharna, A. / Wenchel, L. / Kadavath, H. / Weber, M. / Meier, B. / Peter, M. / Riek, R. / Mezzenga, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qut.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qut.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qut_validation.pdf.gz | 1001.3 KB | Display | wwPDB validaton report |
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Full document | 8qut_full_validation.pdf.gz | 1002.1 KB | Display | |
Data in XML | 8qut_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 8qut_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/8qut ftp://data.pdbj.org/pub/pdb/validation_reports/qu/8qut | HTTPS FTP |
-Related structure data
Related structure data | 18663MC 8qv8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 14720.693 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LYZ / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: P61626 #2: Protein/peptide | Mass: 869.063 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Oryza sativa (Asian cultivated rice) Has ligand of interest | N | |
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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 |
-Sample preparation
Component | Name: lysozyme amyloid fibril / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Oryza sativa (Asian cultivated rice) |
Buffer solution | pH: 7 / Details: 20mM DTT |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 62.79 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 926 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Helical symmerty | Angular rotation/subunit: -1 ° / Axial rise/subunit: 4.78 Å / Axial symmetry: C1 | ||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51695 / Symmetry type: HELICAL | ||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |