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- EMDB-74861: 9.1-Angstrom resolution structure of the portal protein core of b... -

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Basic information

Entry
Database: EMDB / ID: EMD-74861
Title9.1-Angstrom resolution structure of the portal protein core of bacteriophage Sf6 by cryo-electron tomography and sub-tomogram averaging with 538 particles
Map datamasked map from RELION 5 postprocess job
Sample
  • Virus: Shigella phage Sf6 (virus)
Keywordsbacteriophage / shigella / podovirus / VIRUS
Biological speciesShigella phage Sf6 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsTang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 9.1-Angstrom resolution structure of the portal protein core of bacteriophage Sf6 by cryo-electron tomography and sub-tomogram averaging with 538 particles
Authors: Tang L
History
DepositionDec 30, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74861.png

Downloads & links

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Map

FileDownload / File: emd_74861.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked map from RELION 5 postprocess job
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.31 Å/pix.
x 72 pix.
= 310.608 Å		4.31 Å/pix.
x 72 pix.
= 310.608 Å		4.31 Å/pix.
x 72 pix.
= 310.608 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.314 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.09714584 - 0.37071007
Average (Standard dev.)0.0074156127 (±0.031001322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 310.608 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74861_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: unmasked map from RELION 5 postprocess job

Fileemd_74861_additional_1.map
Annotationunmasked map from RELION 5 postprocess job
Projections & Slices
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Histogram

Histogram (log scale)

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Additional map: merged map from relion 5 reconstruct job

Fileemd_74861_additional_2.map
Annotationmerged map from relion 5 reconstruct job
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: half map from relion 5 reconstruct job. Note...

Fileemd_74861_half_map_1.map
Annotationhalf map from relion 5 reconstruct job. Note that the map is noisy and is best viewed with low pass filtration or slight gaussian smoothing in UCSF Chimerax.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map from relion 5 reconstruct job. Note...

Fileemd_74861_half_map_2.map
Annotationhalf map from relion 5 reconstruct job. Note that the map is noisy and is best viewed with low pass filtration or slight gaussian smoothing in UCSF Chimerax.
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)

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Supramolecule #1: Shigella phage Sf6

SupramoleculeName: Shigella phage Sf6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: complete virion 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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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 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
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 reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5)
Details: C12 symmetry was applied to reconstruct the volume.
Number subtomograms used: 538
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) of 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 ...Details: A small set (~30) of 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)
Details: Alignment was first performed with the icosahedral symmetry with rtf refinement and bayesian polishing. The angles were then expanded to the C1 symmetry with the region 5 symmetry_expand ...Details: Alignment was first performed with the icosahedral symmetry with rtf refinement and bayesian polishing. The angles were then expanded to the C1 symmetry with the region 5 symmetry_expand program, followed by 3D classification focused on a 5-fold vertex of the icosahedral phage particle using a manually generated smooth ellipsoidal mask. This generated a set of angles with the tail aligned to the same single 5-fold vertex, which then were used to reconstruct the phage particle in the C12 symmetry.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7sfs


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The portal protein from 7SFS were rigid-body fitted into the map
DetailsRigid body fitting was performed with UCSF Chimerax.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient

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