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- PDB-6rrt: T=4 MS2 Virus-like-particle -

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Basic information

Entry
Database: PDB / ID: 6rrt
TitleT=4 MS2 Virus-like-particle
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / MS2 / T=4 / BACTERIOPHAGE / VLP
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Biological speciesEscherichia phage MS2 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
Authorsde Martin Garrido, N. / Ramlaul, K. / Simpson, P.A. / Crone, M.A. / Freemont, P.S. / Aylett, C.H.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust206212_Z_17_Z United Kingdom
Royal Society206212_Z_17_Z United Kingdom
CitationJournal: Mol Microbiol / Year: 2020
Title: Bacteriophage MS2 displays unreported capsid variability assembling T = 4 and mixed capsids.
Authors: Natàlia de Martín Garrido / Michael A Crone / Kailash Ramlaul / Paul A Simpson / Paul S Freemont / Christopher H S Aylett /
Abstract: Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds ...Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds through a maturation protein incorporated into its capsid. Cryogenic electron microscopy has previously shown that its genome is highly ordered within virions, and that it regulates the assembly process of the capsid. In this study, we have assembled recombinant MS2 capsids with non-genomic RNA containing the capsid incorporation sequence, and investigated the structures formed, revealing that T = 3, T = 4 and mixed capsids between these two triangulation numbers are generated, and resolving structures of T = 3 and T = 4 capsids to 4 Å and 6 Å respectively. We conclude that the basic MS2 capsid can form a mix of T = 3 and T = 4 structures, supporting a role for the ordered genome in favouring the formation of functional T = 3 virions.
History
DepositionMay 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 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
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

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)55,4794
Polymers55,4794
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,328,718240
Polymers3,328,718240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Capsid protein / CP / Coat protein


Mass: 13869.659 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage MS2 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P03612

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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: Escherichia virus MS2 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia virus MS2
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.5 / Details: 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K

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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: 100000 X / Nominal defocus max: -2000 nm / Nominal defocus min: -300 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 80 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 2129
Details: Frames were obtained with a beam-splitter Images were recorded at both 100kx and 150kx and resampled in Fourier space to 100kx for refinement
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameCategoryDetails
1EMANparticle selectionBOXER
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
10RELIONfinal Euler assignmentversion 2.1
12RELION3D reconstructionVersion 2.1
Image processingDetails: Dose weighting was applied with MotionCor2
CTF correctionDetails: Internal in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3499 / Algorithm: FOURIER SPACE
Details: Resolution within a tight mask was 6.16 by FSC 0.143 cut-off while unmasked resolution was 7.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: Dimers were fitted independently
Atomic model buildingPDB-ID: 5TC1

5tc1


Accession code: 5TC1 / Source name: PDB / Type: experimental model

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