+Open data
-Basic information
Entry | Database: PDB / ID: 7uii | ||||||||||||
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Title | Cryo-EM of self-assembled cannula CanA | ||||||||||||
Components | CanA | ||||||||||||
Keywords | PROTEIN FIBRIL / self-assemble / cannula / helical tube / donor strand | ||||||||||||
Biological species | Pyrodictium abyssi (archaea) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||
Authors | Wang, F. / Miller, J.G. / Egelman, E.H. / Conticello, V.P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Cryo-EM of self-assembled cannula CanA Authors: Wang, F. / Miller, J.G. / Egelman, E.H. / Conticello, V.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uii.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uii.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 7uii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uii_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7uii_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7uii_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 7uii_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/7uii ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7uii | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 93 / Rise per n subunits: 1.59 Å / Rotation per n subunits: -173.747 °) |
-Components
#1: Protein | Mass: 19989.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrodictium abyssi (archaea) / Production host: Escherichia coli (E. coli) | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: CanA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Pyrodictium abyssi (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -173.747 ° / Axial rise/subunit: 1.59 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 659059 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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