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Open data
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Basic information
Entry | Database: PDB / ID: 3zue | ||||||
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Title | Rabbit Hemorrhagic Disease Virus (RHDV)capsid protein | ||||||
![]() | CAPSID STRUCTURAL PROTEIN VP60 | ||||||
![]() | VIRUS / CAGE DESIGN / MOLECULAR SWITCH / PROTEIN ENGINEERING / STRUCTURAL POLYMORPHISM / VIRUS ASSEMBLY | ||||||
Function / homology | ![]() calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / host cell cytoplasm / 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 | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.3 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C | ||||||
![]() | Luque, 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. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 64.8 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 856.7 KB | Display | ![]() |
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Full document | ![]() | 856.3 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1933MC ![]() 1934C ![]() 1935C ![]() 1936C ![]() 1937C ![]() 1938C ![]() 1939C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 60264.785 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: WT RABBIT HEMORRHAGIC DISEASE VIRUS VLP / Type: VIRUS |
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Buffer solution | Name: 200 MM NA2HPO4, 200 MM NACL / pH: 6 / Details: 200 MM NA2HPO4, 200 MM NACL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE / Details: LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 recording | Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 116 |
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Processing
EM software | Name: Xmipp / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: PHASE FLIPPING AND AMPLITUDE DECAY | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: 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 building | Protocol: OTHER / Space: REAL / Details: METHOD--CORRELATION | ||||||||||||
Refinement | Highest resolution: 10.3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 10.3 Å
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