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Open data
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Basic information
Entry | Database: PDB / ID: 8iy7 | ||||||
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Title | Cryo-EM structure of DIP-2I8I fibril polymorph1 | ||||||
![]() | GLY-PHI-GLY-ASN-GLY-ASN-GLY-PHI-GLY | ||||||
![]() | PROTEIN FIBRIL / Iodized peptide | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.71 Å | ||||||
![]() | Li, D.N. / Ma, Y.Y. / Li, D. / Dai, B. / Liu, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Cryo-EM structure of DIP-2I8I fibril polymorph1 Authors: Li, D.N. / Ma, Y.Y. / Li, D. / Dai, B. / Liu, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.4 KB | Display | ![]() |
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PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 46.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein/peptide | Mass: 1077.621 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) ![]() Has ligand of interest | Y | |
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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 DIP-2I8I fibril polymorph1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7 |
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: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.15.2_3472: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -1.24 ° / Axial rise/subunit: 4.83 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13423 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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