+Open data
-Basic information
Entry | Database: PDB / ID: 8eld | |||||||||||||||
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Title | Bacteriophage HRP29 Icosohedral Reconstruction | |||||||||||||||
Components |
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Keywords | VIRUS / HRP29 | |||||||||||||||
Function / homology | Uncharacterized protein / Putative capsid protein / Uncharacterized protein Function and homology information | |||||||||||||||
Biological species | Shigella phage Buco (virus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Subramanian, S. / Bergland Drarvik, S.M. / Parent, K.N. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: To Be Published Title: Structure of Shigella bacteriophage HRP29 Authors: Subramanian, S. / Bergland Drarvik, S.M. / Parent, K.N. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eld.cif.gz | 447.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eld.ent.gz | 369.7 KB | Display | PDB format |
PDBx/mmJSON format | 8eld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eld_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8eld_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8eld_validation.xml.gz | 100.8 KB | Display | |
Data in CIF | 8eld_validation.cif.gz | 148.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/8eld ftp://data.pdbj.org/pub/pdb/validation_reports/el/8eld | HTTPS FTP |
-Related structure data
Related structure data | 28226MC 8em6C 8es4C 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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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 36911.305 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JKU4 #2: Protein | Mass: 13021.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JKV2 #3: Protein | Mass: 6424.381 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Shigella phage Buco (virus) / References: UniProt: A0A482JG80 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Shigella phage HRP29 / Type: VIRUS / Entity ID: all / Source: NATURAL | |||||||||||||||
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Source (natural) | Organism: Shigella phage Buco (virus) | |||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION | |||||||||||||||
Natural host | Organism: Shigella flexneri Y | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 33 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38666 / Symmetry type: POINT |