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- PDB-3zue: Rabbit Hemorrhagic Disease Virus (RHDV)capsid protein -

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Basic information

Entry
Database: PDB / ID: 3zue
TitleRabbit Hemorrhagic Disease Virus (RHDV)capsid protein
ComponentsCAPSID STRUCTURAL PROTEIN VP60
KeywordsVIRUS / CAGE DESIGN / MOLECULAR SWITCH / PROTEIN ENGINEERING / STRUCTURAL POLYMORPHISM / VIRUS ASSEMBLY
Function / homology
Function and homology information


calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / viral capsid / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / viral capsid / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / 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. ...: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / 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
Genome polyprotein / Capsid structural protein VP60
Similarity search - Component
Biological speciesRABBIT HEMORRHAGIC DISEASE VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.3 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C
AuthorsLuque, D. / Gonzalez, J.M. / Gomez-Blanco, J. / Marabini, R. / Chichon, J. / Mena, I. / Angulo, I. / Carrascosa, J.L. / Verdaguer, N. / Trus, B.L. ...Luque, D. / Gonzalez, J.M. / Gomez-Blanco, J. / Marabini, R. / Chichon, J. / Mena, I. / Angulo, I. / Carrascosa, J.L. / Verdaguer, N. / Trus, B.L. / Barcena, J. / Caston, J.R.
CitationJournal: J Virol / Year: 2012
Title: Epitope insertion at the N-terminal molecular switch of the rabbit hemorrhagic disease virus T = 3 capsid protein leads to larger T = 4 capsids.
Authors: Daniel Luque / José M González / Josué Gómez-Blanco / Roberto Marabini / Javier Chichón / Ignacio Mena / Iván Angulo / José L Carrascosa / Nuria Verdaguer / Benes L Trus / Juan ...Authors: Daniel Luque / José M González / Josué Gómez-Blanco / Roberto Marabini / Javier Chichón / Ignacio Mena / Iván Angulo / José L Carrascosa / Nuria Verdaguer / Benes L Trus / Juan Bárcena / José R Castón /
Abstract: Viruses need only one or a few structural capsid proteins to build an infectious particle. This is possible through the extensive use of symmetry and the conformational polymorphism of the structural ...Viruses need only one or a few structural capsid proteins to build an infectious particle. This is possible through the extensive use of symmetry and the conformational polymorphism of the structural proteins. Using virus-like particles (VLP) from rabbit hemorrhagic disease virus (RHDV) as a model, we addressed the basis of calicivirus capsid assembly and their application in vaccine design. The RHDV capsid is based on a T=3 lattice containing 180 identical subunits (VP1). We determined the structure of RHDV VLP to 8.0-Å resolution by three-dimensional cryoelectron microscopy; in addition, we used San Miguel sea lion virus (SMSV) and feline calicivirus (FCV) capsid subunit structures to establish the backbone structure of VP1 by homology modeling and flexible docking analysis. Based on the three-domain VP1 model, several insertion mutants were designed to validate the VP1 pseudoatomic model, and foreign epitopes were placed at the N- or C-terminal end, as well as in an exposed loop on the capsid surface. We selected a set of T and B cell epitopes of various lengths derived from viral and eukaryotic origins. Structural analysis of these chimeric capsids further validates the VP1 model to design new chimeras. Whereas most insertions are well tolerated, VP1 with an FCV capsid protein-neutralizing epitope at the N terminus assembled into mixtures of T=3 and larger T=4 capsids. The calicivirus capsid protein, and perhaps that of many other viruses, thus can encode polymorphism modulators that are not anticipated from the plane sequence, with important implications for understanding virus assembly and evolution.
History
DepositionJul 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • 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-1933
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  • Superimposition on EM map
  • EMDB-1933
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Structure viewerMolecule:
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Assembly

Deposited unit
A: CAPSID STRUCTURAL PROTEIN VP60
B: CAPSID STRUCTURAL PROTEIN VP60
C: CAPSID STRUCTURAL PROTEIN VP60


Theoretical massNumber of molelcules
Total (without water)180,7943
Polymers180,7943
Non-polymers00
Water00
1
A: CAPSID STRUCTURAL PROTEIN VP60
B: CAPSID STRUCTURAL PROTEIN VP60
C: CAPSID STRUCTURAL PROTEIN VP60
x 60


Theoretical massNumber of molelcules
Total (without water)10,847,661180
Polymers10,847,661180
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: CAPSID STRUCTURAL PROTEIN VP60
B: CAPSID STRUCTURAL PROTEIN VP60
C: CAPSID STRUCTURAL PROTEIN VP60
x 5


  • icosahedral pentamer
  • 904 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)903,97215
Polymers903,97215
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CAPSID STRUCTURAL PROTEIN VP60
B: CAPSID STRUCTURAL PROTEIN VP60
C: CAPSID STRUCTURAL PROTEIN VP60
x 6


  • icosahedral 23 hexamer
  • 1.08 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,084,76618
Polymers1,084,76618
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 CAPSID STRUCTURAL PROTEIN VP60 / VP1 / Coordinate model: Cα atoms only


Mass: 60264.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RABBIT HEMORRHAGIC DISEASE VIRUS / Strain: AST89 / Cell line (production host): H5 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9YND5, UniProt: Q86119*PLUS

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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: WT RABBIT HEMORRHAGIC DISEASE VIRUS VLP / Type: VIRUS
Buffer solutionName: 200 MM NA2HPO4, 200 MM NACL / pH: 6 / Details: 200 MM NA2HPO4, 200 MM NACL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.26 mm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 116

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Processing

EM softwareName: Xmipp / Category: 3D reconstruction
CTF correctionDetails: PHASE FLIPPING AND AMPLITUDE DECAY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.3 Å / Num. of particles: 5011 / Nominal pixel size: 2.8 Å / Actual pixel size: 2.8 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1933 (DEPOSITION ID: 10153).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--CORRELATION
RefinementHighest resolution: 10.3 Å
Refinement stepCycle: LAST / Highest resolution: 10.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 0 0 1637

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