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- EMDB-48864: MS2-pMS2 Icosahedral Reconstruction -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48864
TitleMS2-pMS2 Icosahedral Reconstruction
Map data
Sample
  • Virus: Escherichia phage MS2 (virus)
    • Protein or peptide: Capsid protein
KeywordsMS2 / VIRUS / 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: 2.4 Å
AuthorsSubramanian S / Makasarashvili N / Garmann RF / Parent KN
Funding support United States, 2 items
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: To Be Published
Title: Measuring the selective packaging of RNA molecules by viral coat proteins in cells
Authors: Rastandeh A / Makasarashvili N / Dhaliwal HK / Subramanian S / Villarreal DA / Baker S / Gamez ET / Parent KN / Garmann RF
History
DepositionFeb 1, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48864.png

Downloads & links

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Map

FileDownload / File: emd_48864.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 499.2 Å		0.83 Å/pix.
x 600 pix.
= 499.2 Å		0.83 Å/pix.
x 600 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.26587403 - 0.749214
Average (Standard dev.)-0.000006968285 (±0.033692516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-299-299-299
Dimensions600600600
Spacing600600600
CellA=B=C: 499.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48864_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48864_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_48864_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: Capsid protein

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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: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
50.0 mMtris(hydroxymethyl)aminomethane
100.0 mMsodium chloride
1.0 mMEDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 728471
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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