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- EMDB-72122: MS2 bacteriophage coat protein after reassembly as a nanocrate (M... -

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Basic information

Entry
Database: EMDB / ID: EMD-72122
TitleMS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled
Map dataSharpened map, output from CryoSPARC non-uniform refinement.
Sample
  • Complex: Escherichia phage MS2 capsid protein
    • Protein or peptide: Capsid protein
  • Ligand: water
KeywordsBacteriophage / VLP / MS2 / nanocrate / VIRUS
Function / homologynegative regulation of viral translation / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / T=3 icosahedral viral capsid / structural molecule activity / RNA binding / identical protein binding / Capsid protein
Function and homology information
Biological speciesEscherichia phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.74 Å
AuthorsZimanyi CM / Bobe D / Jenkins MC / Kopylov M
Funding support United States, 3 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI148382 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA247484 United States
CitationJournal: bioRxiv / Year: 2025
Title: Overcoming air-water interface-induced artifacts in Cryo-EM with protein nanocrates.
Authors: Matthew C Jenkins / Daija Bobe / Jake D Johnston / Jonah Cheung / Akira Karasawa / Christina M Zimanyi / Ömer Dermanci / M G Finn / Alex de Marco / Mykhailo Kopylov /
Abstract: Contact with the air-water interface can bias the orientation of macromolecules during cryo-EM sample preparation, leading to uneven sample distribution, preferred orientation, and damage to the ...Contact with the air-water interface can bias the orientation of macromolecules during cryo-EM sample preparation, leading to uneven sample distribution, preferred orientation, and damage to the molecules of interest. To prevent this, we describe a method to encapsulate target proteins within highly hydrophilic, structurally homogeneous, and stable protein shells, which we refer to as "nanocrates" for this purpose. Here, we describe packaging, data acquisition, and reconstruction of three proof-of-principle examples, each illuminating a different aspect of the method: apoferritin (ApoF, demonstrating high-resolution), thyroglobulin (Tg, solving a known preferred orientation problem), and 7,8-dihydroneopterin aldolase (DHNA, a structure previously uncharacterized by cryo-EM).
History
DepositionAug 13, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72122.png

Downloads & links

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Map

FileDownload / File: emd_72122.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map, output from CryoSPARC non-uniform refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-0.66447973 - 2.2656622
Average (Standard dev.)0.014789989 (±0.10270529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 397.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72122_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map, output from CryoSPARC non-uniform refinement.

Fileemd_72122_additional_1.map
AnnotationUnsharpened map, output from CryoSPARC non-uniform refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map, output from CryoSPARC non-uniform refinement.

Fileemd_72122_half_map_1.map
AnnotationUnsharpened half map, output from CryoSPARC non-uniform refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map, output from CryoSPARC non-uniform refinement.

Fileemd_72122_half_map_2.map
AnnotationUnsharpened half map, output from CryoSPARC non-uniform refinement.
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 capsid protein

EntireName: Escherichia phage MS2 capsid protein
Components
  • Complex: Escherichia phage MS2 capsid protein
    • Protein or peptide: Capsid protein
  • Ligand: water

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Supramolecule #1: Escherichia phage MS2 capsid protein

SupramoleculeName: Escherichia phage MS2 capsid protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Reassembled as a nanocrate with no cargo after disassembly and RNA removal.
Source (natural)Organism: Escherichia phage MS2 (virus)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage MS2 (virus)
Molecular weightTheoretical: 13.738464 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ASNFTQFVLV DNGGTGDVTV APSNFANGVA EWISSNSRSQ AYKVTCSVRQ SSAQNRKYTI KVEVPKVATQ TVGGVELPVA AWRSYLNME LTIPIFATNS DCELIVKAMQ GLLKDGNPIP SAIAANSGIY

UniProtKB: Capsid protein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 228 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8.5 / Details: 100 mM Tris-HCl [pH 8.5], 80 mM KCl, 10 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2860 / Average exposure time: 1.25 sec. / Average electron dose: 54.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 348343
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 1.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 239460
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2izm


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9q1b:
MS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled

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