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- EMDB-3859: Structure of Aeropyrum pernix bacilloform virus 1 APBV1 helical c... -

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Basic information

Entry
Database: EMDB / ID: 3859
TitleStructure of Aeropyrum pernix bacilloform virus 1 APBV1 helical capsid pointy end
Map dataAPBV1 pointy tip
SampleAeropyrum pernix bacilliform virus 1:
virus
SourceAeropyrum pernix bacilliform virus 1
Methodsingle particle reconstruction / cryo EM / 7.2 Å resolution
AuthorsHuiskonen JT / Pchelkine D / Gillum A
CitationJournal: Nat Commun / Year: 2017
Title: Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging.
Authors: Denis Ptchelkine / Ashley Gillum / Tomohiro Mochizuki / Soizick Lucas-Staat / Ying Liu / Mart Krupovic / Simon E V Phillips / David Prangishvili / Juha T Huiskonen
DateDeposition: Sep 6, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Jan 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3859.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.35 Å/pix.
= 432. Å
320 pix
1.35 Å/pix.
= 432. Å
320 pix
1.35 Å/pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.03811019 - 0.08176798
Average (Standard dev.)0.00017475817 (0.0052796844)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 432 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0380.0820.000

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Supplemental data

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Sample components

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Entire Aeropyrum pernix bacilliform virus 1

EntireName: Aeropyrum pernix bacilliform virus 1 / Number of components: 1

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Component #1: virus, Aeropyrum pernix bacilliform virus 1

VirusName: Aeropyrum pernix bacilliform virus 1 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Aeropyrum pernix bacilliform virus 1
Source (natural)Host Species: Aeropyrum pernix (archaea)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: distilled water / pH: 7
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37037 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C5 (5 fold cyclic) / Number of projections: 2572
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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