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

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Basic information

Entry
Database: PDB / ID: 3j1p
TitleAtomic model of rabbit hemorrhagic disease virus
ComponentsMajor capsid protein VP60
KeywordsVIRUS / icosahedral virus / calicivirus / lagovirus
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. / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesRabbit hemorrhagic disease virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsWang, X. / Liu, Y. / 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 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_sheet.number_strands

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5410
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  • Superimposition on EM map
  • EMDB-5410
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein VP60
B: Major capsid protein VP60
C: Major capsid protein VP60


Theoretical massNumber of molelcules
Total (without water)181,1303
Polymers181,1303
Non-polymers00
Water0
1
A: Major capsid protein VP60
B: Major capsid protein VP60
C: Major capsid protein VP60
x 60


Theoretical massNumber of molelcules
Total (without water)10,867,819180
Polymers10,867,819180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein VP60
B: Major capsid protein VP60
C: Major capsid protein VP60
x 5


  • icosahedral pentamer
  • 906 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)905,65215
Polymers905,65215
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein VP60
B: Major capsid protein VP60
C: Major capsid protein VP60
x 6


  • icosahedral 23 hexamer
  • 1.09 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,086,78218
Polymers1,086,78218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Major capsid protein VP60


Mass: 60376.770 Da / Num. of mol.: 3 / Fragment: UNP residues 1766-2344 / Source method: isolated from a natural source / Source: (natural) Rabbit hemorrhagic disease virus / Strain: HYD / References: UniProt: F5BXG7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Wild Rabbit Hemorrhagic Disease Virus (strain HYD) / Type: VIRUS
Molecular weightValue: 10.8 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Oryctolagus cuniculus
Buffer solutionName: TNE buffer / pH: 7 / Details: 50 mM Tris, 50 mM NaCl, 5 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 50 mM Tris, 50 mM NaCl, 5 mM EDTA
Specimen supportDetails: 200 mesh copper grid with holey array carbon support (GiG), glow discharged
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 100 K / Humidity: 100 %
Details: Blot for 3 seconds before plunging into liquid ethane.
Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 22, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Calibrated magnification: 160770 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Liquid nitrogen cooled / Temperature: 85 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3EMAN1.93D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: CTF correction of each whole micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Projection matching and Fourier reconstruction / Resolution: 6.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 26000 / Nominal pixel size: 0.933 Å / Actual pixel size: 0.933 Å / Magnification calibration: cross gating and interpolation
Details: The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom (details about the particle: the particles were selected using an automatic selection program FindEM).
Num. of class averages: 475 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITREALREFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The P domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).
2FLEXIBLE FITREALREFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The S domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).
3OTHERREALREFINEMENT PROTOCOL--Manual building of NTA domain DETAILS--The N-terminal NTA domain was manually built according to the high resolution EM map.
Atomic model building

Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-ID
14EGT

4egt

14EGT1
24EJR

4ejr

24EJR2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms11703 0 0 0 11703

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