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- EMDB-6887: Cryo-EM structure of HBV Cp164 capsid -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-6887
TitleCryo-EM structure of HBV Cp164 capsid
Map dataHBV capsid assembled from core protein-164
SampleHBV core protein-164 != Hepatitis B virus

HBV core protein-164

  • Virus: Hepatitis B virus
    • Protein or peptide: HBV core protein-164
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsHe J / Li Z / Gao Y / Yan D / Sun J / Zhang Q / Liu S
CitationJournal: To Be Published
Title: Insights into the Structural Organization of Carboxy-Terminal Domain via Nuclease Sensitivity of Hepatitis B Virus Capsid
Authors: He J / Li Z / Gao Y / Yan D / Sun J / Zhang Q / Liu S
History
DepositionJan 12, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseMay 2, 2018-
UpdateMay 2, 2018-
Current statusMay 2, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6887.png

Downloads & links

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Map

FileDownload / File: emd_6887.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHBV capsid assembled from core protein-164
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 55. / Movie #1: 55
Minimum - Maximum-121.608270000000005 - 191.98429999999999
Average (Standard dev.)0.3913985 (±16.456509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin282828
Dimensions400400400
Spacing400400400
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z436.000436.000436.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS282828
NC/NR/NS400400400
D min/max/mean-121.608191.9840.391

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Supplemental data

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Sample components

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Entire : HBV core protein-164

EntireName: HBV core protein-164
Components
  • Virus: Hepatitis B virus
    • Protein or peptide: HBV core protein-164

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Escherichia coli (E. coli)

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Macromolecule #1: HBV core protein-164

MacromoleculeName: HBV core protein-164 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus / Strain: adr
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ASVELLSFLP SDFFPSIRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMNLAT WVGSNLEDPA SRELVVSYVN VNMGLKIRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR RRGRSPRRRT PSPR

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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

Concentration15 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17436
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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