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- PDB-7f29: Cryo-EM structure of the fibril formed by disaccharide-modified a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f29 | ||||||
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Title | Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42) | ||||||
![]() | Amyloid-beta A4 protein | ||||||
![]() | PROTEIN FIBRIL / amyloid fibril | ||||||
Function / homology | ![]() signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft ...signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Xia, W.C. / Sun, Y.P. / Liu, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: O-Glycosylation Induces Amyloid-beta To Form New Fibril Polymorphs Vulnerable for Degradation Authors: Liu, D. / Wei, Q. / Xia, W. / He, C. / Zhang, Q. / Huang, L. / Wang, X. / Sun, Y. / Ma, Y. / Zhang, X. / Wang, Y. / Shi, X. / Liu, C. / Dong, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.7 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31428MC 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/peptide | Mass: 3900.440 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-alpha-D-galactopyranose Type: oligosaccharide / Mass: 341.312 Da / Num. of mol.: 6 / Source method: obtained synthetically #3: Chemical | ChemComp-ACY / 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 |
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Sample preparation
Component | Name: Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42) Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: SYNTHETIC |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 179.324 ° / Axial rise/subunit: 2.4 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92523 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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