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- PDB-9n41: MS2-pcoat Icosahedral Reconstruction -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9n41
TitleMS2-pcoat Icosahedral Reconstruction
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / MS2 / VIRUS
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: 2.2 Å
AuthorsSubramanian, S. / Makasarashvili, N. / Garmann, R.F. / Parent, K.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127751 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Measuring the selective packaging of RNA molecules by viral coat proteins in cells.
Authors: Amineh Rastandeh / Nino Makasarashvili / Herman K Dhaliwal / Sherry Baker / Sundharraman Subramanian / Daniel A Villarreal / Elmer I Gamez / Kristin N Parent / Rees F Garmann /
Abstract: Some RNA viruses package their genomes with extraordinary selectivity, assembling protein capsids around their own viral RNA while excluding nearly all host RNA. How the assembling proteins ...Some RNA viruses package their genomes with extraordinary selectivity, assembling protein capsids around their own viral RNA while excluding nearly all host RNA. How the assembling proteins distinguish viral RNA from host RNA is not fully understood, but RNA structure is thought to play a key role. To test this idea, we perform in-cellulo packaging experiments using bacteriophage MS2 coat proteins and a variety of RNA molecules in . In each experiment, plasmid-derived RNA molecules with a specified sequence compete against the cellular transcriptome for packaging by plasmid-derived coat proteins. Following this competition, we quantify the total amount and relative composition of the packaged RNA using electron microscopy, interferometric scattering microscopy, and high-throughput sequencing. By systematically varying the input RNA sequence and measuring changes in packaging outcomes, we are able to directly test competing models of selective packaging. Our results rule out a longstanding model in which selective packaging requires the well-known translational repressor (TR) stem-loop, and instead support more recent models in which selectivity emerges from the collective interactions of multiple coat proteins and multiple stem-loops distributed across the RNA molecule. These findings establish a framework for studying and understanding selective packaging in a range of natural viruses and virus-like particles, and lay the groundwork for engineering synthetic systems that package specific RNA cargoes.
History
DepositionFeb 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,2153
Polymers41,2153
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)2,472,924180
Polymers2,472,924180
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: 13738.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage MS2 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03612
Has protein modificationN

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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 phage MS2 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage MS2 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
150 mMtris(hydroxymethyl)aminomethane1
2100 mMsodium chloride1
31 mMEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50.18 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
13cryoSPARC4.6.03D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313055 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022936
ELECTRON MICROSCOPYf_angle_d0.4164003
ELECTRON MICROSCOPYf_dihedral_angle_d3.658409
ELECTRON MICROSCOPYf_chiral_restr0.043472
ELECTRON MICROSCOPYf_plane_restr0.004520

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