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

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Basic information

Entry
Database: PDB / ID: 8ugq
TitleCryoEM Structure of Maize Streak Virus (MSV) - Geminivirus
Components
  • Capsid protein
  • DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
KeywordsVIRAL 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
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
DNA / Capsid protein
Similarity search - Component
Biological speciesMaize streak virus genotype A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsMcKenna, R. / Bennett, A.B. / Mietzsch, M. / Hull, J.A.
Funding support United States, 1items
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, A.B. / Mietzsch, M. / Hull, J.A.
History
DepositionOct 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
L: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
B: Capsid protein
M: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
C: Capsid protein
N: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
D: Capsid protein
O: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
E: Capsid protein
P: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
F: Capsid protein
Q: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
G: Capsid protein
R: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
H: Capsid protein
S: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
I: Capsid protein
T: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
J: Capsid protein
U: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
K: Capsid protein
V: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)325,05322
Polymers325,05322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Capsid protein / Coat protein / CP


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
DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
Source (natural)Organism: Maize streak virus genotype A (isolate Nigeria) / Strain: isolate Nigeria
Source (recombinant)Organism: Agrobacterium tumefaciens (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Zea mays
Virus shellTriangulation number (T number): 1
Buffer solutionpH: 4
Buffer componentConc.: 0.1 M / Name: Sodium acetate / Formula: NaAc
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3627 nm / Nominal defocus min: 947 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Num. of real images: 1408

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
7Cootmodel fitting
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1408 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingType: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009209930
ELECTRON MICROSCOPYf_angle_d0.977289240
ELECTRON MICROSCOPYf_dihedral_angle_d16.451156830
ELECTRON MICROSCOPYf_chiral_restr0.0531570
ELECTRON MICROSCOPYf_plane_restr0.00633800

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