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- PDB-4ejr: Crystal structure of major capsid protein S domain from rabbit he... -

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Basic information

Entry
Database: PDB / ID: 4ejr
TitleCrystal structure of major capsid protein S domain from rabbit hemorrhagic disease virus
ComponentsMajor capsid protein VP60
KeywordsVIRAL PROTEIN / capsid protein
Function / homology
Function and homology information


viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding ...viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
: / Viral genome-linked protein / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Jelly Rolls - #20 / Helicase, superfamily 3, single-stranded RNA virus ...: / Viral genome-linked protein / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Jelly Rolls - #20 / 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 / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Major capsid protein VP60 / Genome polyprotein
Similarity search - Component
Biological speciesRabbit hemorrhagic disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, F. / Ma, J. / Zhang, K. / Wang, X. / 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, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,4172
Polymers54,4172
Non-polymers00
Water1,40578
1
A: Major capsid protein VP60

A: Major capsid protein VP60


Theoretical massNumber of molelcules
Total (without water)54,4172
Polymers54,4172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area980 Å2
ΔGint-14 kcal/mol
Surface area15910 Å2
MethodPISA
2
B: Major capsid protein VP60

B: Major capsid protein VP60


Theoretical massNumber of molelcules
Total (without water)54,4172
Polymers54,4172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area1130 Å2
ΔGint-15 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.734, 48.362, 65.163
Angle α, β, γ (deg.)90.00, 100.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Major capsid protein VP60


Mass: 27208.283 Da / Num. of mol.: 2 / Fragment: S (inner shell) domain (UNP residues 1-230)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabbit hemorrhagic disease virus / Strain: JX/CHA/97 / Gene: VP60 / Plasmid: pEXS-DH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q3HNQ1, UniProt: Q3HNQ2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: 0.2 M magnesium chloride, 0.1 M HEPES sodium, 30% PEG400, pH 7.0, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24872 / Num. obs: 24815 / % possible obs: 99.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.97 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GH8

2gh8


Resolution: 2→49.35 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24064 1330 5.1 %RANDOM
Rwork0.2005 ---
obs0.20257 24813 99.79 %-
all-24872 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.968 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 0 78 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.9453570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42423.333114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4815356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4891516
X-RAY DIFFRACTIONr_chiral_restr0.1720.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0222052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5591.51630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.63122666
X-RAY DIFFRACTIONr_scbond_it3.823970
X-RAY DIFFRACTIONr_scangle_it5.9254.5904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 81 -
Rwork0.231 1769 -
obs--97.11 %

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