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- EMDB-72999: Sf11 bacteriophage portal -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72999
TitleSf11 bacteriophage portal
Map data
Sample
  • Virus: Shigella phage Sf11 SMD-2017 (virus)
    • Protein or peptide: Sf11 portal
KeywordsSf11 / bacteriophage / VIRUS
Function / homologyProtein of unknown function DUF1073 / Phage portal protein / Anti-CBASS protein Acb1-like N-terminal domain-containing protein
Function and homology information
Biological speciesShigella phage Sf11 SMD-2017 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 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
DepositionOct 1, 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_72999.png

Downloads & links

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Map

FileDownload / File: emd_72999.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-0.33943817 - 0.6919052
Average (Standard dev.)0.0058434284 (±0.038672023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72999_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72999_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_72999_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: Sf11 portal

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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: Sf11 portal

MacromoleculeName: Sf11 portal / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 52.372395 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MSKIDALNAY IRDRVANNNR AIQQQRLCAG GKNLDQKHDR LWTECGYKQE INAEDFRFAY ERYPLANAAV NIVLNKSWHG MPTVLENDA DDEATSPWEK SVNDILKKAL PFIRDADKRN LINRYSALIL QIRDGKQWSE PVDITKTRRI KDKSIVRFIP V WEEQLRVS ...String:
MSKIDALNAY IRDRVANNNR AIQQQRLCAG GKNLDQKHDR LWTECGYKQE INAEDFRFAY ERYPLANAAV NIVLNKSWHG MPTVLENDA DDEATSPWEK SVNDILKKAL PFIRDADKRN LINRYSALIL QIRDGKQWSE PVDITKTRRI KDKSIVRFIP V WEEQLRVS AWNNDETSED YGMPEMYEYQ ESAVEDFDSD GKPERSVQIH PDRIIILAEG SFDGSMFSGV PLLRAGFNSL ID CAKVSGS SAEGLLKNSS RQLNVSFNKD NVSAQSLAQQ MQVPVDELAD LLNENIEMLN SGIDAAMFSF GSDVSVLSTS MSD PEPFMY VAASQFAASV NIPLNSLLGS RSGVLASAND EQSLAMMAMQ RRDGWLDYLV GSFVERLITF GIVDKAPAAG YYCK WNDLL EPTQNDKAEL IVKLAQAAQS AANAGVGQIL TDDEIRGFLG LEPIEMPDGY MEDTPPEGED EDTPV

UniProtKB: Anti-CBASS protein Acb1-like N-terminal domain-containing 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: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 20482
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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