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- EMDB-3521: Near-atomic resolution structure of a plant geminivirus determine... -

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Basic information

Entry
Database: EMDB / ID: 3521
TitleNear-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy
Map data
SampleAfrican cassava mosaic virus - [West Kenya 844]:
virus / Capsid proteinCapsid
Function / homologyGeminivirus AR1 coat protein / Geminivirus AR1/BR1 coat protein / 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
SourceAfrican cassava mosaic virus - [West Kenya 844]
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsBottcher B / Hipp K / Grimm C / Jeske H
CitationJournal: Structure / Year: 2017
Title: Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.
Authors: Katharina Hipp / Clemens Grimm / Holger Jeske / Bettina Böttcher
Abstract: African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its ...African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved.
Validation ReportPDB-ID: 6ek5

SummaryFull reportAbout validation report
DateDeposition: Dec 1, 2016 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Mar 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ek5
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3521.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.57 Å/pix.
= 471. Å
300 pix
1.57 Å/pix.
= 471. Å
300 pix
1.57 Å/pix.
= 471. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.57 Å
Density
Contour Level:0.12 (by author), 0.12 (movie #1):
Minimum - Maximum-0.31652924 - 0.48998
Average (Standard dev.)0.0026929826 (0.023348128)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 471.00003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.571.571.57
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z471.000471.000471.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3170.4900.003

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Supplemental data

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Mask #1

Fileemd_3521_msk_1.map ( map file in CCP4 format, 108001 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3521_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire African cassava mosaic virus - [West Kenya 844]

EntireName: African cassava mosaic virus - [West Kenya 844] / Number of components: 2
MassTheoretical: 3.3 MDa

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Component #1: virus, African cassava mosaic virus - [West Kenya 844]

VirusName: African cassava mosaic virus - [West Kenya 844] / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 3.3 MDa
SpeciesSpecies: African cassava mosaic virus - [West Kenya 844]
Source (natural)Host Species: Manihot esculenta (cassava)

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Component #2: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Recombinant expression: No
MassTheoretical: 24.094891 kDa
Source (engineered)Expression System: African cassava mosaic virus (isolate West Kenyan 844)
Strain: isolate West Kenyan 844

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
Support filmQuantifoil R1.2/1.3 + 2nm C. Glow discharged for 30-60 s with 25-28 MicroAmp (Quorum Tec Mini Sputter coater SC7620) and used within 1 hour
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 1 %
Details: Samples (3 ?l) were applied to the glow discharged grids, incubated for 60 s on the grid, blotted and plunge frozen in liquid ethane using a Vitrobot IV (FEI, Eindhoven, The Netherlands) at 4?C with 100% humidity and blotting from both sides for 3 s with blot force 7

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 94000 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 934
Details: data acquisition with a cs-corrected FEI Titan Krios on a Falcon II direct detector at 300 kV. Data was acquired at a primary magnification of 94,000 (calibrated pixel size of 1.57 A) and with a total dose of 25 e/A2 in 17 frames. In total 1,108 movies were recorded of which 934 movies were used for further processing. The movie frames were averaged after motion correction and dose weightin

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D5 (2*5 fold dihedral) / Number of projections: 24451
Details: Images were motion correted and weighted for dose damage; the CTF was determined with CTFFIND 3
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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