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- EMDB-3857: Structure of Aeropyrum pernix bacilliform virus 1 APBV1 helical capsid -

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Basic information

Entry
Database: EMDB / ID: 3857
TitleStructure of Aeropyrum pernix bacilliform virus 1 APBV1 helical capsid
SampleAeropyrum pernix bacilliform virus 1
SourceAeropyrum pernix bacilliform virus 1 / virus / image: Aeropyrum pernix K1
Map dataAPBV1 helical capsid
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsHuiskonen JT / Ptchelkine D / Gillum A
CitationNat Commun, 2017, 8, 1436-1436

Nat Commun, 2017, 8, 1436-1436 Yorodumi Papers
Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging.
Denis Ptchelkine / Ashley Gillum / Tomohiro Mochizuki / Soizick Lucas-Staat / Ying Liu / Mart Krupovic / Simon E V Phillips / David Prangishvili / Juha T Huiskonen

Validation ReportPDB-ID: 5oxe

SummaryFull reportAbout validation report
DateDeposition: Sep 6, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 22, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5oxe
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5oxe
  • Imaged by Jmol
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Downloads & links

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Map

Fileemd_3857.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.35 Å/pix.
= 243. Å
180 pix
1.35 Å/pix.
= 243. Å
180 pix
1.35 Å/pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.11308209 - 0.18221602
Average (Standard dev.)-0.00078583346 (0.015131986)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin000
Limit179179179
Spacing180180180
CellA=B=C: 243 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z243.000243.000243.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1130.182-0.001

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Supplemental data

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Mask #1

Fileemd_3857_msk_1.map ( map file in CCP4 format, 23329 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsAPBV1 helical capsid. mask used for FSC
Space group number1

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Mask #1~

Fileemd_3857_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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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: 2

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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 / virus / image: Aeropyrum pernix K1
Source (natural)Host Species: Aeropyrum pernix / archaea / thermophilic / アエロピルム・ペルニックス / image: Aeropyrum pernix K1

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Component #2: protein, Major virion protein

ProteinName: Major virion protein / Recombinant expression: No
MassTheoretical: 8.272858 kDa
SourceSpecies: Aeropyrum pernix bacilliform virus 1 / virus / image: Aeropyrum pernix K1

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Experimental details

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Sample preparation

Specimen statehelical array
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: K2 Summit / 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: 94645
3D reconstructionAlgorithm: FOURIER SPACE / Software: SPRING / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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