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- EMDB-4174: CryoEM structure of Ageratum Yellow Vein virus (AYVV) -

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Basic information

Entry
Database: EMDB / ID: EMD-4174
TitleCryoEM structure of Ageratum Yellow Vein virus (AYVV)
Map dataAgeratum Yellow Vein virus cryoEM density map
Sample
  • Virus: Ageratum yellow vein virus
    • Protein or peptide: Capsid proteinCapsid
    • DNA: ssDNA loop
    • Protein or peptide: coat protein subunit I
    • Protein or peptide: coat protein subunit H
    • DNA: ssDNA loop associated with subunit H
KeywordsAYVV / geminivirus / ssDNA / gemini / VIRUS
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
Biological speciesAgeratum yellow vein virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHesketh EL / Saunders K
Funding support United Kingdom, 5 items
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, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJun 27, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f2s
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6f2s
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4174.png

Downloads & links

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Map

FileDownload / File: emd_4174.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAgeratum Yellow Vein virus cryoEM density map
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.17064932 - 0.2795285
Average (Standard dev.)0.0006186557 (±0.011320367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 477.12003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z477.120477.120477.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.1710.2800.001

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Supplemental data

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Additional map: Ageratum Yellow Vein virus unsharpened

Fileemd_4174_additional.map
AnnotationAgeratum Yellow Vein virus unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ageratum yellow vein virus

EntireName: Ageratum yellow vein virus
Components
  • Virus: Ageratum yellow vein virus
    • Protein or peptide: Capsid proteinCapsid
    • DNA: ssDNA loop
    • Protein or peptide: coat protein subunit I
    • Protein or peptide: coat protein subunit H
    • DNA: ssDNA loop associated with subunit H

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Supramolecule #1: Ageratum yellow vein virus

SupramoleculeName: Ageratum yellow vein virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 44560 / Sci species name: Ageratum yellow vein virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Ageratum (plant)
Molecular weightTheoretical: 251 KDa

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Ageratum yellow vein virus
Molecular weightTheoretical: 22.500703 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: PDVPKGCEGP CKVQSYEQRH DISHVGKVLC VSDVTRGNGL THRVGKRFCV KSVYVLGKIW MDENIKTKNH TNTVMFYLVR DRRPFGTAM DFGQVFNMYD NEPSTATIKN DLRDRYQVLR KFTSTVTGGQ YASKEQALVK KFMKINNYVV YNHQEAAKYD N HTENALLL ...String:
PDVPKGCEGP CKVQSYEQRH DISHVGKVLC VSDVTRGNGL THRVGKRFCV KSVYVLGKIW MDENIKTKNH TNTVMFYLVR DRRPFGTAM DFGQVFNMYD NEPSTATIKN DLRDRYQVLR KFTSTVTGGQ YASKEQALVK KFMKINNYVV YNHQEAAKYD N HTENALLL YMACTHASNP VYATLKIRIY FYDSVQN

UniProtKB: Capsid protein

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Macromolecule #3: coat protein subunit I

MacromoleculeName: coat protein subunit I / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ageratum yellow vein virus
Molecular weightTheoretical: 23.644094 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: RLYRMYRTPD VPKGCEGPCK VQSYEQRHDI SHVGKVLCVS DVTRGNGLTH RVGKRFCVKS VYVLGKIWMD ENIKTKNHTN TVMFYLVRD RRPFGTAMDF GQVFNMYDNE PSTATIKNDL RDRYQVLRKF TSTVTGGQYA SKEQALVKKF MKINNYVVYN H QEAAKYDN ...String:
RLYRMYRTPD VPKGCEGPCK VQSYEQRHDI SHVGKVLCVS DVTRGNGLTH RVGKRFCVKS VYVLGKIWMD ENIKTKNHTN TVMFYLVRD RRPFGTAMDF GQVFNMYDNE PSTATIKNDL RDRYQVLRKF TSTVTGGQYA SKEQALVKKF MKINNYVVYN H QEAAKYDN HTENALLLYM ACTHASNPVY ATLKIRIYFY DSVQN

UniProtKB: Capsid protein

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Macromolecule #4: coat protein subunit H

MacromoleculeName: coat protein subunit H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ageratum yellow vein virus
Molecular weightTheoretical: 25.664473 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: NRRRTWTNRP MYRKPRLYRM YRTPDVPKGC EGPCKVQSYE QRHDISHVGK VLCVSDVTRG NGLTHRVGKR FCVKSVYVLG KIWMDENIK TKNHTNTVMF YLVRDRRPFG TAMDFGQVFN MYDNEPSTAT IKNDLRDRYQ VLRKFTSTVT GGQYASKEQA L VKKFMKIN ...String:
NRRRTWTNRP MYRKPRLYRM YRTPDVPKGC EGPCKVQSYE QRHDISHVGK VLCVSDVTRG NGLTHRVGKR FCVKSVYVLG KIWMDENIK TKNHTNTVMF YLVRDRRPFG TAMDFGQVFN MYDNEPSTAT IKNDLRDRYQ VLRKFTSTVT GGQYASKEQA L VKKFMKIN NYVVYNHQEA AKYDNHTENA LLLYMACTHA SNPVYATLKI RIYFYDSVQN

UniProtKB: Capsid protein

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Macromolecule #2: ssDNA loop

MacromoleculeName: ssDNA loop / type: dna / ID: 2 / Number of copies: 10 / Classification: DNA
Source (natural)Organism: Ageratum yellow vein virus
Molecular weightTheoretical: 2.05139 KDa
SequenceString:
(DC)(DA)(DA)(DC)(DC)(DA)(DC)

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Macromolecule #5: ssDNA loop associated with subunit H

MacromoleculeName: ssDNA loop associated with subunit H / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Ageratum yellow vein virus
Molecular weightTheoretical: 1.762208 KDa
SequenceString:
(DC)(DA)(DA)(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

BufferpH: 7 / Component - Concentration: 100.0 mM / Component - Formula: NaPo4 / Component - Name: Sodium phosphate
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 2000 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa / Details: PELCO easiglow
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 78.0 K / Max: 78.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 12028 / Average exposure time: 2.0 sec. / Average electron dose: 110.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 116240
Startup modelType of model: OTHER
Details: Negative stain electron microscopy map produced in house
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 64932
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

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

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