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- EMDB-6935: Cryo-EM structure of PCV3 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-6935
TitleCryo-EM structure of PCV3 VLP
Map dataCryo-EM structure of PCV3 VLP
Sample
  • Virus: Porcine circovirus
    • Other: PCV3 capsid protein
Function / homologyCircovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / Cap
Function and homology information
Biological speciesPorcine circovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsMo X / Yuan AY
CitationJournal: to be published
Title: Cryo-EM Structure of Virus-like-particle of Porcine Circovirus type 3 reveals an T=1 symmetry icosahedral particle
Authors: Mo X / Yuan AY
History
DepositionMar 31, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 11, 2018-
UpdateApr 11, 2018-
Current statusApr 11, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.36
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6935.png

Downloads & links

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Map

FileDownload / File: emd_6935.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of PCV3 VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 200 pix.
= 338. Å		1.69 Å/pix.
x 200 pix.
= 338. Å		1.69 Å/pix.
x 200 pix.
= 338. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.36 / Movie #1: 2.36
Minimum - Maximum-5.758031 - 6.432379
Average (Standard dev.)0.015526598 (±0.75232685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 338.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z338.000338.000338.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-5.7586.4320.016

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Supplemental data

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Sample components

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Entire : Porcine circovirus

EntireName: Porcine circovirus
Components
  • Virus: Porcine circovirus
    • Other: PCV3 capsid protein

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Supramolecule #1: Porcine circovirus

SupramoleculeName: Porcine circovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Porcine circovirus 3 capsid protein / NCBI-ID: 46221 / Sci species name: Porcine circovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Molecular weightExperimental: 1.7 MDa

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Macromolecule #1: PCV3 capsid protein

MacromoleculeName: PCV3 capsid protein / type: other / ID: 1 / Classification: other
Source (natural)Organism: Porcine circovirus
SequenceString: MRHRAIFRRR PRPRRRRRHR RRYVRRKLFI RRPTAGTYYT KKYSTMNVIS VGTPQNNKPW HANHFITRLN EWETAISFEY YKILKMKVT LSPVISPAQQ TKTMFGHTAI DLDGAWTTNT WLQDDPYAES STRKVMTSKK KHSRYFTPKP ILAGTTSAHP G QSLFFFSR ...String:
MRHRAIFRRR PRPRRRRRHR RRYVRRKLFI RRPTAGTYYT KKYSTMNVIS VGTPQNNKPW HANHFITRLN EWETAISFEY YKILKMKVT LSPVISPAQQ TKTMFGHTAI DLDGAWTTNT WLQDDPYAES STRKVMTSKK KHSRYFTPKP ILAGTTSAHP G QSLFFFSR PTPWLNTYDP TVQWGALLWS IYVPEKTGMT DFYGTKEVWI RYKSVL

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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

Concentration1 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
500.0 mMNaClsodium chloride
20.0 mMPBphosphate buffer

Details: 20mM PB(pH 6.5), 500mM NaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before pluning.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN
TemperatureMin: 70.0 K / Max: 70.0 K
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 5 / Number real images: 90 / Average exposure time: 1.0 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 47000 / Illumination mode: OTHER / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 12000
CTF correctionSoftware - Name: EMAN2 (ver. 2.1)
Final reconstructionNumber classes used: 30 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 5200
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 32 / Avg.num./class: 200 / Software - Name: EMAN2 (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 300

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