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- EMDB-45163: Bacteriophage Sf14 Capsid Empty Icosahedral reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-45163
TitleBacteriophage Sf14 Capsid Empty Icosahedral reconstruction
Map data
Sample
  • Virus: Shigella phage Sf14 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Putative structural protein
    • Protein or peptide: Putative tail protein
KeywordsSf14 / VIRUS
Function / homology
Function and homology information


host cell cytoplasm
Similarity search - Function
Major capsid protein GpE / Phage major capsid protein E / : / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Major capsid protein GpE / Phage major capsid protein E / : / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative tail protein / Major capsid protein / Putative structural protein
Similarity search - Component
Biological speciesShigella phage Sf14 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSubramanian S / Kerns HR / Braverman SG / Doore SM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI170608 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116789 United States
CitationJournal: Commun Biol / Year: 2025
Title: The structure of Shigella virus Sf14 reveals the presence of two decoration proteins and two long tail fibers.
Authors: Sundharraman Subramanian / Hailey R Kerns / Samantha G Braverman / Sarah M Doore /
Abstract: Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we ...Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we determined high-resolution structures of the Sf14 capsid and neck, along with a moderate-resolution structure of the whole Sf14 tail and baseplate. These structures indicate the capsid has not one, but two different types of decoration proteins: a trimeric β-tulip lattice that covers the entire capsid and a set of Hoc-like proteins that bind preferentially to hexamers at the quasi-3-fold axes of symmetry. The neck also contains two sets of whiskers oriented in opposite directions, and the tail has two types of long tail fibers which may bind different receptors. Based on homology and phylogenetic analysis, Sf14 may be the product of multiple horizontal gene transfer events. The structures presented here can be used to investigate further hypotheses of phage structure-function relationships and structural diversity.
History
DepositionMay 31, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45163.png

Downloads & links

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Map

FileDownload / File: emd_45163.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 1000 pix.
= 1224. Å		1.22 Å/pix.
x 1000 pix.
= 1224. Å		1.22 Å/pix.
x 1000 pix.
= 1224. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.224 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.651
Minimum - Maximum-2.864013 - 5.9227223
Average (Standard dev.)0.00069008296 (±0.24873541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-499-499-499
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1224.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45163_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45163_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45163_half_map_2.map
Projections & Slices
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Sample components

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Entire : Shigella phage Sf14

EntireName: Shigella phage Sf14 (virus)
Components
  • Virus: Shigella phage Sf14 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Putative structural protein
    • Protein or peptide: Putative tail protein

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Supramolecule #1: Shigella phage Sf14

SupramoleculeName: Shigella phage Sf14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2024304 / Sci species name: Shigella phage Sf14 / 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

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 41.595992 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MLTNSEKSRF FLADLTGEVQ SIPNTYGYIS GLGLFRSAPQ TQTTFLMDLT DWDISLLDAV DRTSRKAETS APERVRQISF PMMYFKEVE SITPDEIQGV RQPGTANELT TEAVVRAKKL MKIRTKFDIT REFLFMQALK GKVIDANGVL YADLYKQFDV T KKTIYFDL ...String:
MLTNSEKSRF FLADLTGEVQ SIPNTYGYIS GLGLFRSAPQ TQTTFLMDLT DWDISLLDAV DRTSRKAETS APERVRQISF PMMYFKEVE SITPDEIQGV RQPGTANELT TEAVVRAKKL MKIRTKFDIT REFLFMQALK GKVIDANGVL YADLYKQFDV T KKTIYFDL DNPNSDIDAH IEDLRMHMED EAKTGTVING EEIHIVVDRT FFSKLIKHPK IRDAYLAQQT PLAWQQITGS LR TGGTDGV QAHMNRFYYG GVVFVQYNGK FKDKRGKTHT LVSIDGVSDT NVGVGHAFPN VAMLGEANNI FEVAYAPCPK MGY ANTLGQ ELYVFEYEKD RDEGIDFEAH SYMLPYCTRP QLLVDVRSDA E

UniProtKB: Major capsid protein

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Macromolecule #2: Putative structural protein

MacromoleculeName: Putative structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 13.574381 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString:
MAYQGFTKLG EREPLNDIIL WEEITPTGHS RKEYAPVAST EYRVGEVLKA DGSKVAAGQE AQADSVCIVN FYADLQLSYH GQLKVVGIY RDAELKDLLK LESGVDAAAV KSALKAKGID FVPTGL

UniProtKB: Putative structural protein

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Macromolecule #3: Putative tail protein

MacromoleculeName: Putative tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 39.336539 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MIKAKTYPDF KEFVKDFVAN VKAGKRYDFR KYQEAVLPLT YSSPWPESDI PEVTDFNYTP DYTVPFSEEL LYSVGAQMRT ADFFMDLQY AIINGKDVDT VYCEWLARVK PFSMLNAKLK DSAQPPVITT QPTGGAVNEG SAINLSIVAT NATSYQWKKG S SDISGATS ...String:
MIKAKTYPDF KEFVKDFVAN VKAGKRYDFR KYQEAVLPLT YSSPWPESDI PEVTDFNYTP DYTVPFSEEL LYSVGAQMRT ADFFMDLQY AIINGKDVDT VYCEWLARVK PFSMLNAKLK DSAQPPVITT QPTGGAVNEG SAINLSIVAT NATSYQWKKG S SDISGATS ATYTKAGAVP ADAGSYTCVV TNDVGSTTSD AAVITINPLP VITTQPTSKA VNESSTLTLS VVATGATSYQ WK KNGTNIS GATSATYSKA NAKTTDAGSY TCVVTNAVGS VTSNAATVTI NPLPVITVQP QDQDLTVGQT LTISITATGA TGY QWRKGN SNISGATSAT YTKASVTTAD DGNYDCVVTN AVGSVTSHQA KVQVTA

UniProtKB: Putative tail 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:
ConcentrationFormulaName
10.0 mMTristris(hydroxymethyl)aminomethane
10.0 mMMgCl2magnesium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 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: NONE / Details: Full capsid was used as the initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98511
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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