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- EMDB-8325: Beta-propiolactone treated coxsackievirus A16 empty procapsid -

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Basic information

Database: EMDB / ID: 8325
TitleBeta-propiolactone treated coxsackievirus A16 empty procapsid
SourceCOXSACKIEVIRUS A16 / virus
Map dataBeta-propiolactone treated coxsackievirus A16 empty procapsid
Methodsingle particle (icosahedral) reconstruction, at 6.5 Å resolution
AuthorsChen F / Yao C
CitationTo Be Published

To Be Published Search PubMed
Structural alteration and surface modifi cation of coxsackievirus A16 capsids by beta-propiolactone treatment
Fan C / Ye XH / Ku ZI / Liu Q / Xu C / Cong Y / Huang Z

Validation ReportPDB-ID: 5tsk

SummaryFull report
PDB-ID: 5tsl

SummaryFull report
About validation report
DateDeposition: Aug 12, 2016 / Header (metadata) release: Oct 12, 2016 / Map release: Feb 1, 2017 / Last update: Mar 15, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5tsk
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5tsl
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links


Fileemd_8325.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.1 Å/pix.
= 440. Å
400 pix
1.1 Å/pix.
= 440. Å
400 pix
1.1 Å/pix.
= 440. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.1 Å
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.33193296 - 0.3592689
Average (Standard dev.)3.0325617E-5 (0.034534447)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 440 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z-220.000-220.000-220.000
length x/y/z440.000440.000440.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-200-200-200
D min/max/mean-0.3280.3550.000

Supplemental data

Sample components


EntireName: COXSACKIEVIRUS A16 / Number of components: 1
MassTheoretical: 5 MDa

Component #1: virus, COXSACKIEVIRUS A16

VirusName: COXSACKIEVIRUS A16 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SPECIES
MassTheoretical: 5 MDa
SpeciesSpecies: COXSACKIEVIRUS A16 / virus
Source (natural)Host Species: Homo sapiens / human / Wikipedia

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.0032 mg/ml / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 % / Details: blot for 2 seconds

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: 57000 X (nominal) / Cs: 0.007 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 70 - 90 K)
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1350
Details: Images were recorded on a Falcon II direct electron detector in the 18-frame movie mode

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 1642
3D reconstructionSoftware: jspr
CTF correction: CTF fitting was automatically performed using fitctf2.py program in jspr
Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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