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Open data
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Basic information
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Title | CryoEM Structure of Maize Streak Virus (MSV) - Geminivirus | |||||||||
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![]() | Maize streak virus - [Nigeria] != Maize streak virus genotype A (isolate Nigeria) Maize streak virus - [Nigeria]
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![]() | Plant / ssDNA / Icosahedron / capsid / VIRAL PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
![]() | McKenna R / Bennett AB / Mietzsch M / Hull JA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The two states of Maize Streak Virus (MSV) Geminivirus Architecture Authors: McKenna R / Bennett AB / Mietzsch M / Hull JA | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 589.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
Images | ![]() | 35.3 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 379 MB 379 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ugqMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_42232_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42232_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Maize streak virus - [Nigeria]
Entire | Name: Maize streak virus - [Nigeria] |
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Components |
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-Supramolecule #1: Maize streak virus genotype A (isolate Nigeria)
Supramolecule | Name: Maize streak virus genotype A (isolate Nigeria) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Gemini capsid is a Pseudo T=1 icosahedron. The structure contains both protein and ssDNA. NCBI-ID: 10823 Sci species name: Maize streak virus genotype A (isolate Nigeria) Sci species strain: isolate Nigeria / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.880529 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSTSKRKRGD DSNWSKRVTK KKPSSAGLKR AGSKADRPSL QIQTLQHAGT TMITVPSGGV CDLINTYARG SDEGNRHTSE TLTYKIAID YHFVADAAAC RYSNTGTGVM WLVYDTTPGG QAPTPQTIFA YPDTLKAWPA TWKVSRELCH RFVVKRRWLF N METDGRIG ...String: MSTSKRKRGD DSNWSKRVTK KKPSSAGLKR AGSKADRPSL QIQTLQHAGT TMITVPSGGV CDLINTYARG SDEGNRHTSE TLTYKIAID YHFVADAAAC RYSNTGTGVM WLVYDTTPGG QAPTPQTIFA YPDTLKAWPA TWKVSRELCH RFVVKRRWLF N METDGRIG SDIPPSNASW KPCKRNIYFH KFTSGLGVRT QWKNVTDGGV GAIQRGALYM VIAPGNGLTF TAHGQTRLYF KS VGN UniProtKB: Capsid protein |
-Macromolecule #2: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
Macromolecule | Name: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3') / type: dna / ID: 2 / Number of copies: 11 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 2.669778 KDa |
Sequence | String: (DC)(DG)(DA)(DA)(DC)(DC)(DC)(DC)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 4 / Component - Concentration: 0.1 M / Component - Formula: NaAc / Component - Name: Sodium acetate |
Grid | Model: C-flat / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Number real images: 1408 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6270000000000002 µm / Nominal defocus min: 0.9470000000000001 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 1408 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Initial model | Chain - Initial model type: in silico model |
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Refinement | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-8ugq: |