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- EMDB-73070: Structure of bacteriophage Sf6 at 7.26 Angstrom resolution by cry... -

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Basic information

Entry
Database: EMDB / ID: EMD-73070
TitleStructure of bacteriophage Sf6 at 7.26 Angstrom resolution by cryo-electron tomography and sub-tomogram averaging with 159 particles (9540 averaging units due to the icosahedral symmetry)
Map data7.26A map from 159 particles by cryoET and sub-tomogram averaging
Sample
  • Virus: Shigella phage Sf6 (virus)
    • Other: bacteriophage Sf6 complete virion
Keywordsbacteriophage / shigella / podovirus / VIRUS
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / Gene 5 protein
Function and homology information
Biological speciesShigella flexneri (bacteria) / Shigella phage Sf6 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 7.26 Å
AuthorsTang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of bacteriophage Sf6 at 7.26 Angstrom resolution by cryo-electron tomography and sub-tomogram
Authors: Tang L
History
DepositionOct 8, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73070.png

Downloads & links

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Map

FileDownload / File: emd_73070.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation7.26A map from 159 particles by cryoET and sub-tomogram averaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 384 pix.
= 828.288 Å		2.16 Å/pix.
x 384 pix.
= 828.288 Å		2.16 Å/pix.
x 384 pix.
= 828.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.157 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.626
Minimum - Maximum-3.9639933 - 5.7584004
Average (Standard dev.)0.017059838 (±0.26821)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 828.288 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73070_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_73070_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map from a relion5 Reconstruct job

Fileemd_73070_half_map_1.map
Annotationhalf map from a relion5 Reconstruct job
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map from a relion5 Reconstruct job

Fileemd_73070_half_map_2.map
Annotationhalf map from a relion5 Reconstruct job
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Shigella phage Sf6

EntireName: Shigella phage Sf6 (virus)
Components
  • Virus: Shigella phage Sf6 (virus)
    • Other: bacteriophage Sf6 complete virion

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Supramolecule #1: Shigella phage Sf6

SupramoleculeName: Shigella phage Sf6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: complete vision purified from infected Shigella hosts
NCBI-ID: 2905959 / Sci species name: Shigella phage Sf6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 19 MDa
Virus shellShell ID: 1 / Name: gp5 / Diameter: 690.0 Å / T number (triangulation number): 7

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Macromolecule #1: bacteriophage Sf6 complete virion

MacromoleculeName: bacteriophage Sf6 complete virion / type: other / ID: 1 / Details: capsid protein gp5 / Classification: other
Source (natural)Organism: Shigella flexneri (bacteria)
SequenceString: MPNNLDSNVS QIVLKKFLPG FMSDLVLAKT VDRQLLAGEI NSSTGDSVSF KRPHQFSSLR TPTGDISGQN KNNLISGKAT GRVGNYITVA VEYQQLEEAI KLNQLEEILA PVRQRIVTDL ETELAHFMMN NGALSLGSPN TPITKWSDVA QTASFLKDLG VNEGENYAVM ...String:
MPNNLDSNVS QIVLKKFLPG FMSDLVLAKT VDRQLLAGEI NSSTGDSVSF KRPHQFSSLR TPTGDISGQN KNNLISGKAT GRVGNYITVA VEYQQLEEAI KLNQLEEILA PVRQRIVTDL ETELAHFMMN NGALSLGSPN TPITKWSDVA QTASFLKDLG VNEGENYAVM DPWSAQRLAD AQTGLHASDQ LVRTAWENAQ IPTNFGGIRA LMSNGLASRT QGAFGGTLTV KTQPTVTYNA VKDSYQFTVT LTGATASVTG FLKAGDQVKF TNTYWLQQQT KQALYNGATP ISFTATVTAD ANSDSGGDVT VTLSGVPIYD TTNPQYNSVS RQVEAGDAVS VVGTASQTMK PNLFYNKFFC GLGSIPLPKL HSIDSAVATY EGFSIRVHKY ADGDANVQKM RFDLLPAYVC FNPHMGGQFF GNP

UniProtKB: Gene 5 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4 / Component:
ConcentrationName
10.0 mMTris-HCl
1.0 mMMgCl2
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 1 / Average exposure time: 0.4 sec. / Average electron dose: 3.0 e/Å2 / Details: 11 tilt series were collected.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number subtomograms used: 159
ExtractionNumber tomograms: 11 / Number images used: 637
Reference model: ab initio model from manually picked particles
Method: template matching / Software: (Name: RELION (ver. 5), EMAN2 (ver. 2.99))
Details: A small set (~30) particles were manually picked from a tilt series with EMAN2, which were used to generate an ab initial model. This model was used to pick particles in all tilt series by ...Details: A small set (~30) particles were manually picked from a tilt series with EMAN2, which were used to generate an ab initial model. This model was used to pick particles in all tilt series by template matching with EMAN2. Particle coordinates were exported to Relion 5.
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.5)
Details: CTF correction was done with CtfFind4.1.5 wrapped in Relion5.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 5)
Details: All particles were classified into the best 3D class.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5l35


Chain - Source name: Other / Chain - Initial model type: experimental model / Details: models from 5L35 were fitted into the map
RefinementProtocol: RIGID BODY FIT

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