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- EMDB-42246: Cryo-EM structure of Maize Streak Virus (MSV) - single head Gemin... -

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Basic information

Entry
Database: EMDB / ID: EMD-42246
TitleCryo-EM structure of Maize Streak Virus (MSV) - single head Geminivirus
Map data
SampleMaize streak virus - [Nigeria] != Maize streak virus genotype A (isolate Nigeria)

Maize streak virus - [Nigeria]

  • Virus: Maize streak virus genotype A (isolate Nigeria)
    • Protein or peptide: Capsid protein
  • Protein or peptide: genomic DNA
Keywordsgeminivirus / single-head / maize / icosahedron / VIRUS-DNA complex
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
Geminivirus MSV 27Kd coat protein / Geminivirus AR1/BR1 coat protein / Geminivirus coat protein/nuclear export factor BR1 family / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesMaize streak virus genotype A (isolate Nigeria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsBennett AB / McKenna R / Mietzsch M / Hull JA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1563234 United States
CitationJournal: To Be Published
Title: The Two States of MSV Gemini Capsid Assembly
Authors: Bennett AD / McKenna R
History
DepositionOct 6, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42246.png

Downloads & links

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Map

FileDownload / File: emd_42246.map.gz / Format: CCP4 / Size: 201.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.01 Å/pix.
x 375 pix.
= 378.75 Å		1.01 Å/pix.
x 375 pix.
= 378.75 Å		1.01 Å/pix.
x 375 pix.
= 378.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-7.63375 - 17.2666
Average (Standard dev.)0.000000003780883 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-187-187-187
Dimensions375375375
Spacing375375375
CellA=B=C: 378.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42246_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42246_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Maize streak virus - [Nigeria]

EntireName: Maize streak virus - [Nigeria]
Components
  • Virus: Maize streak virus genotype A (isolate Nigeria)
    • Protein or peptide: Capsid protein
  • Protein or peptide: genomic DNA

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Supramolecule #1: Maize streak virus genotype A (isolate Nigeria)

SupramoleculeName: Maize streak virus genotype A (isolate Nigeria) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10823
Sci species name: Maize streak virus genotype A (isolate Nigeria)
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Zea mays (maize)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Maize streak virus genotype A (isolate Nigeria) / Strain: isolate Nigeria
Molecular weightTheoretical: 26.880529 KDa
Recombinant expressionOrganism: Agrobacterium tumefaciens (bacteria)
SequenceString: 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

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Macromolecule #2: genomic DNA

MacromoleculeName: genomic DNA / type: protein_or_peptide / ID: 2 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Maize streak virus genotype A (isolate Nigeria)
Molecular weightTheoretical: 2.755787 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DT)(DC)(DC)(DC)(DA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43111
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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