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- EMDB-5410: Cryo-electron microscopic reconstruction of wild rabbit hemorrhag... -

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Basic information

Entry
Database: EMDB / ID: EMD-5410
TitleCryo-electron microscopic reconstruction of wild rabbit hemorrhagic disease virus
Map dataReconstruction of wild rabbit hemorrhagic disease virus; The final map was sharpened using b factor -300 A2 to 4.5 angstrom and low passed to 5 angstrom.
Sample
  • Sample: Wild Rabbit Hemorrhagic Disease Virus (strain HYD)
  • Virus: Rabbit hemorrhagic disease virus
Keywordscalicivirus / Lagovirus / rabbit hemorrhagic disease
Function / homology
Function and homology information


calicivirin / RNA-protein covalent cross-linking / nucleoside-triphosphate phosphatase / host cell cytoplasm / RNA helicase activity / membrane => GO:0016020 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...calicivirin / RNA-protein covalent cross-linking / nucleoside-triphosphate phosphatase / host cell cytoplasm / RNA helicase activity / membrane => GO:0016020 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein ...Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesRabbit hemorrhagic disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsWang X / Xu F / Liu J / Gao B / Zhang K / Zhai Y / Ma J / Hu Z / Pang X / Zheng D ...Wang X / Xu F / Liu J / Gao B / Zhang K / Zhai Y / Ma J / Hu Z / Pang X / Zheng D / Pang H / Sun F
CitationJournal: PLoS Pathog / Year: 2013
Title: Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.
Authors: Xue Wang / Fengting Xu / Jiasen Liu / Bingquan Gao / Yanxin Liu / Yujia Zhai / Jun Ma / Kai Zhang / Timothy S Baker / Klaus Schulten / Dong Zheng / Hai Pang / Fei Sun /
Abstract: Rabbit hemorrhagic disease, first described in China in 1984, causes hemorrhagic necrosis of the liver. Its etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus ...Rabbit hemorrhagic disease, first described in China in 1984, causes hemorrhagic necrosis of the liver. Its etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus in the family Caliciviridae. The detailed molecular structure of any lagovirus capsid has yet to be determined. Here, we report a cryo-electron microscopic (cryoEM) reconstruction of wild-type RHDV at 6.5 Å resolution and the crystal structures of the shell (S) and protruding (P) domains of its major capsid protein, VP60, each at 2.0 Å resolution. From these data we built a complete atomic model of the RHDV capsid. VP60 has a conserved S domain and a specific P2 sub-domain that differs from those found in other caliciviruses. As seen in the shell portion of the RHDV cryoEM map, which was resolved to ~5.5 Å, the N-terminal arm domain of VP60 folds back onto its cognate S domain. Sequence alignments of VP60 from six groups of RHDV isolates revealed seven regions of high variation that could be mapped onto the surface of the P2 sub-domain and suggested three putative pockets might be responsible for binding to histo-blood group antigens. A flexible loop in one of these regions was shown to interact with rabbit tissue cells and contains an important epitope for anti-RHDV antibody production. Our study provides a reliable, pseudo-atomic model of a Lagovirus and suggests a new candidate for an efficient vaccine that can be used to protect rabbits from RHDV infection.
History
DepositionApr 7, 2012-
Header (metadata) releaseApr 19, 2012-
Map releaseJan 30, 2013-
UpdateFeb 6, 2013-
Current statusFeb 6, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j1p
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j1p
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5410.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of wild rabbit hemorrhagic disease virus; The final map was sharpened using b factor -300 A2 to 4.5 angstrom and low passed to 5 angstrom.
Voxel sizeX=Y=Z: 0.933 Å
Density
Contour LevelBy AUTHOR: 2.6 / Movie #1: 2.6
Minimum - Maximum-8.73291588 - 16.738216399999999
Average (Standard dev.)0.12011245 (±1.83568513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 447.84003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9330.9330.933
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z447.840447.840447.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-240-240-240
NC/NR/NS480480480
D min/max/mean-8.73316.7380.120

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Supplemental data

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Sample components

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Entire : Wild Rabbit Hemorrhagic Disease Virus (strain HYD)

EntireName: Wild Rabbit Hemorrhagic Disease Virus (strain HYD)
Components
  • Sample: Wild Rabbit Hemorrhagic Disease Virus (strain HYD)
  • Virus: Rabbit hemorrhagic disease virus

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Supramolecule #1000: Wild Rabbit Hemorrhagic Disease Virus (strain HYD)

SupramoleculeName: Wild Rabbit Hemorrhagic Disease Virus (strain HYD) / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 10.8 MDa

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Supramolecule #1: Rabbit hemorrhagic disease virus

SupramoleculeName: Rabbit hemorrhagic disease virus / type: virus / ID: 1 / Name.synonym: RHDV / Details: HYD strain and gene bank number is AEB26305. / NCBI-ID: 11976 / Sci species name: Rabbit hemorrhagic disease virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: RHDV
Host (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: VERTEBRATES
Molecular weightTheoretical: 10.8 MDa
Virus shellShell ID: 1 / Name: VP60 / Diameter: 440 Å / T number (triangulation number): 3

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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 / Details: 50mM Tris, 50mM NaCl, 5mM EDTA
GridDetails: 200 mesh copper grid with holey array carbon support (GiG), glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 160770 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureAverage: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Legacy - Electron beam tilt params: 0
DateJan 22, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1100 / Average electron dose: 20 e/Å2 / Bits/pixel: 32
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correction of each whole micrograph
Final two d classificationNumber classes: 475
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1.9, Spider
Details: The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom.
Number images used: 26000
DetailsThe particles were selected using an automatic selection program FindEM.

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A
SoftwareName: Chimera
DetailsProtocol: Rigid body. The P domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j1p:
Atomic model of rabbit hemorrhagic disease virus

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Atomic model buiding 2

Initial modelPDB ID:

Chain - Chain ID: A
SoftwareName: Chimera
DetailsProtocol: Rigid body. The S domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j1p:
Atomic model of rabbit hemorrhagic disease virus

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