+Open data
-Basic information
Entry | Database: PDB / ID: 8ugq | ||||||
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Title | CryoEM Structure of Maize Streak Virus (MSV) - Geminivirus | ||||||
Components |
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Keywords | VIRAL PROTEIN / Plant / ssDNA / Icosahedron / capsid | ||||||
Function / homology | Function and homology information T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | ||||||
Biological species | Maize streak virus genotype A | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å | ||||||
Authors | McKenna, R. / Bennett, A.B. / Mietzsch, M. / Hull, J.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The two states of Maize Streak Virus (MSV) Geminivirus Architecture Authors: McKenna, R. / Bennett, A.B. / Mietzsch, M. / Hull, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ugq.cif.gz | 454.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ugq.ent.gz | 377.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ugq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ugq_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ugq_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ugq_validation.xml.gz | 81.2 KB | Display | |
Data in CIF | 8ugq_validation.cif.gz | 110.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/8ugq ftp://data.pdbj.org/pub/pdb/validation_reports/ug/8ugq | HTTPS FTP |
-Related structure data
Related structure data | 42232MC 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: 26880.529 Da / Num. of mol.: 11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maize streak virus genotype A (isolate Nigeria) Strain: isolate Nigeria / Gene: V1 / Production host: Agrobacterium tumefaciens (bacteria) / References: UniProt: P06448 #2: DNA chain | Mass: 2669.778 Da / Num. of mol.: 11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maize streak virus genotype A (isolate Nigeria) Strain: isolate Nigeria / Production host: Agrobacterium tumefaciens (bacteria) |
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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: Maize streak virus - [Nigeria] / Type: VIRUS Details: Gemini capsid is a Pseudo T=1 icosahedron. The structure contains both protein and ssDNA. Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Maize streak virus genotype A (isolate Nigeria) / Strain: isolate Nigeria |
Source (recombinant) | Organism: Agrobacterium tumefaciens (bacteria) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Zea mays |
Virus shell | Triangulation number (T number): 1 |
Buffer solution | pH: 4 |
Buffer component | Conc.: 0.1 M / Name: Sodium acetate / Formula: NaAc |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: C-flat |
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: 3627 nm / Nominal defocus min: 947 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: 1408 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: D5 (2x5 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1408 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Atomic model building | Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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