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- EMDB-70309: Sf11 capsid Icosahedral Reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-70309
TitleSf11 capsid Icosahedral Reconstruction
Map data
Sample
  • Virus: Shigella phage Sf11 SMD-2017 (virus)
    • Protein or peptide: Major capsid protein gp39
    • Protein or peptide: Putative capsid decoration protein gp40
KeywordsSf11 / bacteriophage / VIRUS
Function / homologyProtein of unknown function DUF6260 / Family of unknown function (DUF6260) / Major capsid protein / Putative capsid decoration protein
Function and homology information
Biological speciesShigella phage Sf11 SMD-2017 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSubramanian S / Parent KN
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: To Be Published
Title: Structure of Shigella bacteriophage Sf11
Authors: Subramanian S / Dover JA / Parent KN
History
DepositionApr 24, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70309.png

Downloads & links

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Map

FileDownload / File: emd_70309.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.)
1.67 Å/pix.
x 600 pix.
= 1000.8 Å		1.67 Å/pix.
x 600 pix.
= 1000.8 Å		1.67 Å/pix.
x 600 pix.
= 1000.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.47
Minimum - Maximum-2.1449852 - 3.7565968
Average (Standard dev.)0.0032453202 (±0.1695219)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-299-299-299
Dimensions600600600
Spacing600600600
CellA=B=C: 1000.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70309_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70309_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70309_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 : Shigella phage Sf11 SMD-2017

EntireName: Shigella phage Sf11 SMD-2017 (virus)
Components
  • Virus: Shigella phage Sf11 SMD-2017 (virus)
    • Protein or peptide: Major capsid protein gp39
    • Protein or peptide: Putative capsid decoration protein gp40

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Supramolecule #1: Shigella phage Sf11 SMD-2017

SupramoleculeName: Shigella phage Sf11 SMD-2017 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2282196 / Sci species name: Shigella phage Sf11 SMD-2017 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri Y (bacteria)

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Macromolecule #1: Major capsid protein gp39

MacromoleculeName: Major capsid protein gp39 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 39.727578 KDa
SequenceString: MEKIIFTKDL VANSAVVADQ WNHLKIDRKV FVNAENALAK KYALNATALV TKDYWRDVDN VTTRVFRNEA GQDMMADLMG IAANINIGK TVAISRIASD AGKVVRTLSG QEPEDLDKTR YDYTGDVIPI FKTGYSREWR ELLGMQAEGF DPLLDDQANV T FNLRSDMA ...String:
MEKIIFTKDL VANSAVVADQ WNHLKIDRKV FVNAENALAK KYALNATALV TKDYWRDVDN VTTRVFRNEA GQDMMADLMG IAANINIGK TVAISRIASD AGKVVRTLSG QEPEDLDKTR YDYTGDVIPI FKTGYSREWR ELLGMQAEGF DPLLDDQANV T FNLRSDMA QYLLTGDQTL NVNGVYTGYG ITNHPNTIQV NLNASGGLNI DLQTATPDEI VTFFNQDFQA ILDAQNVFEQ VT LWVSPAV RRSFMRPYSN AAGFKGGTVE QYITQFGNGR IGKIGTNFLL TGNHFVGYVR NDMYIRPRVA QPVSTYAAAR ANP HDNFNF LVWSAMGLQI RKDFTGKSKV FNGYGTQTPQ

UniProtKB: Major capsid protein

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Macromolecule #2: Putative capsid decoration protein gp40

MacromoleculeName: Putative capsid decoration protein gp40 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 15.871763 KDa
SequenceString:
MATIRYGTII GGPARKNDPQ IREGIMNAAL QPGALVTFND DDKIIAHATA GGQGFPYVLQ HNYLGGGDVS EAVPANATGM AVQCEFGVT YHALVAQSSV LKKGTPLASN GAGALKVAGD GDNILFYSYE TYTVASDGAE LVAVRRAGNA SMPAGA

UniProtKB: Putative capsid decoration 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
10.0 mMtris(hydroxymethyl)aminomethane
10.0 mMmagnesium chloride
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 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.45 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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