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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 / homologyGeminivirus AR1 coat protein / Geminivirus AR1/BR1 coat protein / Viral coat protein subunit / Geminivirus coat protein/nuclear export factor BR1 family / T=1 icosahedral viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell nucleus / structural molecule activity / DNA binding ...Geminivirus AR1 coat protein / Geminivirus AR1/BR1 coat protein / Viral coat protein subunit / Geminivirus coat protein/nuclear export factor BR1 family / T=1 icosahedral viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell nucleus / structural molecule activity / DNA binding / metal ion binding / Capsid protein
Function and homology information
Specimen sourceAgeratum yellow vein virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsHesketh, E.L. / Saunders, K. / Fisher, C. / Potze, J. / Stanley, J. / Lomonossoff, G.P. / Ranson, N.A.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 27, 2017 / Release: Jun 27, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 27, 2018Structure modelrepositoryInitial release
1.1Jul 4, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
1.2Oct 17, 2018Structure modelData collection / Refinement descriptionrefine

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Structure visualization

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  • Biological unit as complete point assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-4174
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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
Polyers274,09122
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
Polyers2,740,910220
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

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Components

#1: Protein/peptide
Capsid protein / Capsid / Coat protein


Mass: 22500.703 Da / Num. of mol.: 9 / 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: (gene. exp.) Ageratum yellow vein virus / Production host: Nicotiana benthamiana (plant)
#3: Protein/peptide coat protein subunit I / Coat protein


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


Mass: 25664.473 Da / Num. of mol.: 1 / 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: (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 / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ageratum yellow vein virus / Type: VIRUS / Entity ID: 1, 2, 3, 4, 5 / 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 / Virus isolate: SPECIES / Virus 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
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / 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 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78 kelvins / Temperature (min): 78 kelvins
Image recordingAverage exposure time: 2 sec. / Electron dose: 110 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number 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
9RELION2.0initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.11model refinement
14REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 116240
SymmetryPoint symmetry: D5
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 64932 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT
RefineCorrelation coeff Fo to Fc: 0.8 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 20.039 / Overall SU ML: 0.273 / Overall ESU R: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 97.466 Å2 / Aniso B11: -1.21 Å2 / Aniso B12: - Å2 / Aniso B13: - Å2 / Aniso B22: -0.95 Å2 / Aniso B23: -0.01 Å2 / Aniso B33: 2.16 Å2
Least-squares processR factor R work: 0.33242 / R factor obs: 0.33242 / Highest resolution: 3.3 Å / Lowest resolution: 477.16 Å / Number reflection obs: 6333908 / Percent reflection obs: 1
Number of atoms included #1Total: 19170
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01919738
ELECTRON MICROSCOPYr_bond_other_d0.0030.02017927
ELECTRON MICROSCOPYr_angle_refined_deg1.0881.86326929
ELECTRON MICROSCOPYr_angle_other_deg1.3993.00041127
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.7525.0002165
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.32123.448899
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.38515.0003175
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.38315.000132
ELECTRON MICROSCOPYr_chiral_restr0.0840.2002861
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.02021414
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0204990
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_refined6.38688.19022402
ELECTRON MICROSCOPYr_long_range_B_other6.38688.19222403
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.3 Å / R factor R work: 0.476 / Lowest resolution: 3.386 Å / Number reflection R free: 0 / Number reflection R work: 469490 / Total number of bins used: 20 / Percent reflection obs: 1

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