+Open data
-Basic information
Entry | Database: PDB / ID: 8fyw | |||||||||
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Title | Cryo-EM Structure of genome containing AAV2 | |||||||||
Components | Capsid protein VP1 | |||||||||
Keywords | VIRUS / capsid / genome / assembly / symmetry | |||||||||
Function / homology | Function and homology information symbiont entry into host cell via permeabilization of host membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | adeno-associated virus 2 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Bennett, A.D. / Mckenna, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Cryo-EM Structure of genome containing AAV2 Authors: Bennett, A.D. / Mckenna, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fyw.cif.gz | 5.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fyw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fyw_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 8fyw_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 8fyw_validation.xml.gz | 654.7 KB | Display | |
Data in CIF | 8fyw_validation.cif.gz | 1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/8fyw ftp://data.pdbj.org/pub/pdb/validation_reports/fy/8fyw | HTTPS FTP |
-Related structure data
Related structure data | 29598MC 8fz0C 8fznC 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: 82031.352 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) adeno-associated virus 2 / Gene: VP1 / Production host: Baculoviridae (virus) / References: UniProt: P03135 #2: Chemical | ChemComp-D5M / Has ligand of interest | Y | |
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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: adeno-associated virus 2 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 3.9 MDa / Experimental value: NO |
Source (natural) | Organism: adeno-associated virus 2 |
Source (recombinant) | Organism: Baculovirus expression vector pCTdual |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION |
Natural host | Organism: Homo sapiens |
Virus shell | Name: capsid / Diameter: 26 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 7.3 / Details: 1X PBS, 1 mM MgCl2, 2.5 mM KCl pH7.3 |
Buffer component | Conc.: 1 mM / Name: TD / Formula: PBS-MK |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Num. of real images: 1674 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3838 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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