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- PDB-6f2s: CryoEM structure of Ageratum Yellow Vein virus (AYVV) -

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Basic information

Entry
Database: PDB / ID: 6f2s
TitleCryoEM structure of Ageratum Yellow Vein virus (AYVV)
Components
  • Capsid proteinCapsid
  • coat protein subunit H
  • coat protein subunit I
  • ssDNA loop
  • ssDNA loop associated with subunit H
KeywordsVIRUS / AYVV / geminivirus / ssDNA / gemini
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral penetration into host nucleus / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding / metal ion binding
Similarity search - Function
Geminivirus AR1 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 speciesAgeratum yellow vein virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHesketh, E.L. / Saunders, K. / Fisher, C. / Potze, J. / Stanley, J. / Lomonossoff, G.P. / Ranson, N.A.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L021250/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L020955/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004596/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012523/1 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: The 3.3 Å structure of a plant geminivirus using cryo-EM.
Authors: Emma L Hesketh / Keith Saunders / Chloe Fisher / Joran Potze / John Stanley / George P Lomonossoff / Neil A Ranson /
Abstract: Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. ...Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. However, despite their importance to agricultural economies and fundamental biological interest, the details of how this is realized in 3D remain unknown. Here we report the structure of Ageratum yellow vein virus at 3.3 Å resolution, using single-particle cryo-electron microscopy, together with an atomic model that shows that the N-terminus of the single capsid protein (CP) adopts three different conformations essential for building the interface between geminate halves. Our map also contains density for ~7 bases of single-stranded DNA bound to each CP, and we show that the interactions between the genome and CPs are different at the interface than in the rest of the capsid. With additional mutagenesis data, this suggests a central role for DNA binding-induced conformational change in directing the assembly of geminate capsids.
History
DepositionNov 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
L: ssDNA loop
B: Capsid protein
M: ssDNA loop
F: Capsid protein
Q: ssDNA loop
E: Capsid protein
P: ssDNA loop
D: Capsid protein
O: ssDNA loop
C: Capsid protein
N: ssDNA loop
K: Capsid protein
V: ssDNA loop
J: Capsid protein
U: ssDNA loop
I: coat protein subunit I
T: ssDNA loop
H: coat protein subunit H
S: ssDNA loop associated with subunit H
G: Capsid protein
R: ssDNA loop


Theoretical massNumber of molelcules
Total (without water)274,09122
Polymers274,09122
Non-polymers00
Water0
1
A: Capsid protein
L: ssDNA loop
B: Capsid protein
M: ssDNA loop
F: Capsid protein
Q: ssDNA loop
E: Capsid protein
P: ssDNA loop
D: Capsid protein
O: ssDNA loop
C: Capsid protein
N: ssDNA loop
K: Capsid protein
V: ssDNA loop
J: Capsid protein
U: ssDNA loop
I: coat protein subunit I
T: ssDNA loop
H: coat protein subunit H
S: ssDNA loop associated with subunit H
G: Capsid protein
R: ssDNA loop
x 10


Theoretical massNumber of molelcules
Total (without water)2,740,910220
Polymers2,740,910220
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation10
2


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D5 (2x5 fold dihedral))

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Components

#1: Protein
Capsid protein / Capsid / Coat protein


Mass: 22500.703 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ageratum yellow vein virus / Gene: V1 / Production host: Nicotiana benthamiana (plant) / References: UniProt: W5RUR4
#2: DNA chain
ssDNA loop


Mass: 2051.390 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ageratum yellow vein virus / Production host: Nicotiana benthamiana (plant)
#3: Protein coat protein subunit I / Coat protein


Mass: 23644.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ageratum yellow vein virus / Gene: V1 / Production host: Nicotiana benthamiana (plant) / References: UniProt: W5RUR4
#4: Protein coat protein subunit H / Coat protein


Mass: 25664.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ageratum yellow vein virus / Gene: V1 / Production host: Nicotiana benthamiana (plant) / References: UniProt: W5RUR4
#5: DNA chain ssDNA loop associated with subunit H


Mass: 1762.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ageratum yellow vein virus / Production host: Nicotiana benthamiana (plant)

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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: Ageratum yellow vein virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.251 MDa
Source (natural)Organism: Ageratum yellow vein virus
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Ageratum
Buffer solutionpH: 7
Buffer componentConc.: 100 mM / Name: Sodium phosphate / Formula: NaPo4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: PELCO easiglow / Grid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 300 nm / Calibrated defocus max: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78 K / Temperature (min): 78 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 110 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12028

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Processing

SoftwareName: REFMAC / Version: 5.8.0107 / Classification: refinement
EM software
IDNameVersionCategory
2EPU1.7image acquisition
4Gctf0.5CTF correction
7Coot0.8.8model fitting
9RELION2initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.11model refinement
14REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 116240
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64932 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementResolution: 3.3→477.16 Å / Cor.coef. Fo:Fc: 0.8 / SU B: 20.039 / SU ML: 0.273 / ESU R: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.33242 --
obs0.33242 6333908 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.466 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0 Å2-0 Å2
2---0.95 Å2-0.01 Å2
3---2.16 Å2
Refinement stepCycle: 1 / Total: 19170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01919738
ELECTRON MICROSCOPYr_bond_other_d0.0030.0217927
ELECTRON MICROSCOPYr_angle_refined_deg1.0881.86326929
ELECTRON MICROSCOPYr_angle_other_deg1.399341127
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.75252165
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.32123.448899
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.385153175
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.38315132
ELECTRON MICROSCOPYr_chiral_restr0.0840.22861
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0221414
ELECTRON MICROSCOPYr_gen_planes_other0.0010.024990
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.7399.6548693
ELECTRON MICROSCOPYr_mcbond_other1.7389.6548692
ELECTRON MICROSCOPYr_mcangle_it3.05814.48210847
ELECTRON MICROSCOPYr_mcangle_other3.05814.48210848
ELECTRON MICROSCOPYr_scbond_it2.0289.98411045
ELECTRON MICROSCOPYr_scbond_other2.0289.98411044
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.68214.85616082
ELECTRON MICROSCOPYr_long_range_B_refined6.38688.1922402
ELECTRON MICROSCOPYr_long_range_B_other6.38688.19222403
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.476 469490 -
Rfree-0 -
obs--100 %

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