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- EMDB-70484: Cryo-EM structure of the assembled MS2 CPM58 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-70484
TitleCryo-EM structure of the assembled MS2 CPM58 VLP
Map data
Sample
  • Virus: Escherichia phage MS2 (virus)
    • Protein or peptide: MS2 CPM58
Keywordsbacteriophage / circular permutation / virus like particle
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsLiang S / Jung J / Tullman-Ercek D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CBET-2043973. United States
CitationJournal: ACS Nano / Year: 2025
Title: Synthetic Rewiring of Virus-like Particles via Circular Permutation Enables Modular Peptide Display and Protein Encapsulation.
Authors: Shiqi Liang / Kaavya Butaney / Daniel de Castro Assumpção / James Jung / Nolan W Kennedy / Danielle Tullman-Ercek /
Abstract: Virus-like particles (VLPs) are self-assembling nanoparticles derived from viruses with the potential as scaffolds for myriad applications. They are also excellent testbeds for engineering protein ...Virus-like particles (VLPs) are self-assembling nanoparticles derived from viruses with the potential as scaffolds for myriad applications. They are also excellent testbeds for engineering protein superstructures. Engineers often employ techniques such as amino acid substitutions and insertions/deletions. Yet evolution also utilizes circular permutation, a powerful natural strategy that has not been fully explored in engineering self-assembling protein nanoparticles. Here, we demonstrate this technique using the MS2 VLP as a model self-assembling proteinaceous nanoparticle. We constructed a comprehensive circular permutation library of the fused MS2 coat protein dimer construct. The strategy revealed terminal locations, validated via cryo-electron microscopy, that enabled C-terminal peptide tagging and led to a protein encapsulation strategy via covalent bonding - a feature the native coat protein does not permit. Our systematic study demonstrates the power of circular permutation for engineering features as well as quantitatively and systematically exploring VLP structural determinants.
History
DepositionMay 2, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70484.png

Downloads & links

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Map

FileDownload / File: emd_70484.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 512 pix.
= 457.728 Å		0.89 Å/pix.
x 512 pix.
= 457.728 Å		0.89 Å/pix.
x 512 pix.
= 457.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.894 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.9632446 - 2.6391625
Average (Standard dev.)0.005894183 (±0.0953204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 457.728 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70484_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70484_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage MS2

EntireName: Escherichia phage MS2 (virus)
Components
  • Virus: Escherichia phage MS2 (virus)
    • Protein or peptide: MS2 CPM58

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Supramolecule #1: Escherichia phage MS2

SupramoleculeName: Escherichia phage MS2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12022 / Sci species name: Escherichia phage MS2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Molecular weightTheoretical: 2.4696 MDa
Virus shellShell ID: 1 / Name: CPM58 VLP / Diameter: 300.0 Å / T number (triangulation number): 3

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Macromolecule #1: MS2 CPM58

MacromoleculeName: MS2 CPM58 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage MS2 (virus)
Molecular weightTheoretical: 27.458957 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YTIKVEVPKV ATQTVGGVEL PVAAWRSYLN MELTIPIFAT NSDCELIVKA MQGLLKDGNP IPSAIAANSG IYASNFTQFV LVDNGGTGD VTVAPSNFAN GVAEWISSNS RSQAYKVTCS VRQSSAQNRK YTIKVEVPKV ATQTVGGVEL PVAAWRSYLN M ELTIPIFA ...String:
YTIKVEVPKV ATQTVGGVEL PVAAWRSYLN MELTIPIFAT NSDCELIVKA MQGLLKDGNP IPSAIAANSG IYASNFTQFV LVDNGGTGD VTVAPSNFAN GVAEWISSNS RSQAYKVTCS VRQSSAQNRK YTIKVEVPKV ATQTVGGVEL PVAAWRSYLN M ELTIPIFA TNSDCELIVK AMQGLLKDGN PIPSAIAANS GIYASNFTQF VLVDNGGTGD VTVAPSNFAN GVAEWISSNS RS QAYKVTC SVRQSSAQNR K

UniProtKB: Capsid protein, Capsid protein, Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 77.0 K
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 5849 / Average exposure time: 5.33 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 539975
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 109941
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1zdi


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9oh5:
Cryo-EM structure of the assembled MS2 CPM58 VLP

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