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- EMDB-42232: CryoEM Structure of Maize Streak Virus (MSV) - Geminivirus -

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Basic information

Entry
Database: EMDB / ID: EMD-42232
TitleCryoEM Structure of Maize Streak Virus (MSV) - 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
    • DNA: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
KeywordsPlant / ssDNA / Icosahedron / capsid / VIRAL PROTEIN
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: 3.17 Å
AuthorsMcKenna R / Bennett AB / Mietzsch M / Hull JA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF DMS 1563234 United States
CitationJournal: To Be Published
Title: The two states of Maize Streak Virus (MSV) Geminivirus Architecture
Authors: McKenna R / Bennett AB / Mietzsch M / Hull JA
History
DepositionOct 5, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42232.png

Downloads & links

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Map

FileDownload / File: emd_42232.map.gz / Format: CCP4 / Size: 634.7 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 550 pix.
= 555.5 Å		1.01 Å/pix.
x 550 pix.
= 555.5 Å		1.01 Å/pix.
x 550 pix.
= 555.5 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 EMDB: 5.0
Minimum - Maximum-10.602963000000001 - 23.530087999999999
Average (Standard dev.)-0.000000009798859 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-275-275-275
Dimensions550550550
Spacing550550550
CellA=B=C: 555.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42232_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_42232_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
    • DNA: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')

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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: 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
Host (natural)Organism: Zea mays (maize)
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / 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: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')

MacromoleculeName: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3') / type: dna / ID: 2 / Number of copies: 11 / Classification: DNA
Source (natural)Organism: Maize streak virus genotype A (isolate Nigeria) / Strain: isolate Nigeria
Molecular weightTheoretical: 2.669778 KDa
SequenceString:
(DC)(DG)(DA)(DA)(DC)(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 / Component - Concentration: 0.1 M / Component - Formula: NaAc / Component - Name: Sodium acetate
GridModel: C-flat / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Number real images: 1408 / 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 / 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 modelType of model: INSILICO MODEL
Final reconstructionApplied 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 assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

Initial modelChain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ugq:
CryoEM Structure of Maize Streak Virus (MSV) - Geminivirus

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