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- EMDB-6212: CryoEM reconstruction of Kaposi's sarcoma-associated herpesvirus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6212
TitleCryoEM reconstruction of Kaposi's sarcoma-associated herpesvirus SCP-null mutant (KSHV-SCPnull)
Map dataCryoEM reconstruction of KSHV-SCPnull mutant
Sample
  • Sample: Kaposi's sarcoma-associated herpesvirus (KSHV) with a null mutation for the smallest capsid protein (SCP)
  • Virus: Human herpesvirus 8
Keywordsherpesvirus / gammaherpesvirus / the smallest capsid protein / cementing protein
Biological speciesHuman herpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsDai XH / Gong DY / Xiao YC / Wu TT / Sun R / Zhou ZH
CitationJournal: PROC.NAT.ACAD.SCI.USA / Year: 2015
Title: CryoEM and mutagenesis reveal that the smallest capsid protein cements and stabilizes Kaposi's sarcoma-associated herpesvirus capsid.
Authors: Dai X / Gong D / Xiao Y / Wu TT / Sun R / Zhou ZH
History
DepositionDec 8, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseFeb 4, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_6212.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of KSHV-SCPnull mutant
Voxel sizeX=Y=Z: 3.789 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-7.03667116 - 6.59614563
Average (Standard dev.)0.01376059 (±0.99512851)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-360
Dimensions480480480
Spacing480480480
CellA=B=C: 1818.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.7893.7893.789
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z1818.7201818.7201818.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS-240-240-360
NC/NR/NS480480480
D min/max/mean-7.0376.5960.014

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Supplemental data

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Sample components

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Entire : Kaposi's sarcoma-associated herpesvirus (KSHV) with a null mutati...

EntireName: Kaposi's sarcoma-associated herpesvirus (KSHV) with a null mutation for the smallest capsid protein (SCP)
Components
  • Sample: Kaposi's sarcoma-associated herpesvirus (KSHV) with a null mutation for the smallest capsid protein (SCP)
  • Virus: Human herpesvirus 8

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Supramolecule #1000: Kaposi's sarcoma-associated herpesvirus (KSHV) with a null mutati...

SupramoleculeName: Kaposi's sarcoma-associated herpesvirus (KSHV) with a null mutation for the smallest capsid protein (SCP)
type: sample / ID: 1000 / Oligomeric state: icosahedral virus / Number unique components: 1

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Supramolecule #1: Human herpesvirus 8

SupramoleculeName: Human herpesvirus 8 / type: virus / ID: 1 / Name.synonym: Kaposi's sarcoma-associated herpesvirus
Details: A stop codon was inserted near the 5'-terminus of the SCP gene (ORF65) to eliminate SCP expression.
NCBI-ID: 37296 / Sci species name: Human herpesvirus 8 / Sci species strain: BAC16 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Kaposi's sarcoma-associated herpesvirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: capsid / Diameter: 1350 Å / T number (triangulation number): 16

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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

BufferpH: 7.4 / Details: PBS
GridDetails: Quantifoil R2/1-Cu200
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJun 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 82 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79176 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each Particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: IMIRS, EMAN1 / Number images used: 137

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