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- EMDB-72124: MS2 bacteriophage coat protein with waters modeled -

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Basic information

Entry
Database: EMDB / ID: EMD-72124
TitleMS2 bacteriophage coat protein 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.75 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: To Be Published
Title: Overcoming air-water interface-induced artifacts in Cryo-EM with protein nanocrates
Authors: Jenkins MC / Bobe D / Johnston JD / Cheung J / Karasawa A / Zimanyi CM / Dermanci O / Finn MG / de Marco A / Kopylov M
History
DepositionAug 13, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72124.png

Downloads & links

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Map

FileDownload / File: emd_72124.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: 0.65
Minimum - Maximum-0.90712833 - 3.2598372
Average (Standard dev.)0.01786455 (±0.15010376)
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_72124_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_72124_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_72124_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_72124_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: Purified after recombinant expression in E. coli.
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: 265 / 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: 4960 / Average exposure time: 1.2 sec. / Average electron dose: 52.36 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: 233748
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: 1.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 106754
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:

9q1b


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

PDB-9q1d:
MS2 bacteriophage coat protein with waters modeled

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