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- EMDB-45162: Bacteriophage Sf14 neck C6 reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-45162
TitleBacteriophage Sf14 neck C6 reconstruction
Map data
Sample
  • Virus: Shigella phage Sf14 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Phage protein
    • Protein or peptide: Head-closure protein
    • Protein or peptide: gp119
    • Protein or peptide: gp40
    • Protein or peptide: Putative structural protein
    • Protein or peptide: gp127
    • Protein or peptide: Phage protein
KeywordsSf14 / VIRUS
Function / homology
Function and homology information


: / Phage neck terminator protein / Protein of unknown function DUF935 / Structural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Portal protein of Mu bacteriophage / Bacteriophage PhiTE tail tube protein / Protein of unknown function (DUF3383)
Similarity search - Domain/homology
Phage protein / Uncharacterized protein / Head-closure protein / Phage protein / Phage neck terminator protein gp12-like domain-containing protein / Uncharacterized protein / Putative portal protein / Putative structural protein
Similarity search - Component
Biological speciesShigella phage Sf14 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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_45162.png

Downloads & links

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Map

FileDownload / File: emd_45162.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.)
0.82 Å/pix.
x 600 pix.
= 489.6 Å		0.82 Å/pix.
x 600 pix.
= 489.6 Å		0.82 Å/pix.
x 600 pix.
= 489.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.816 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.242
Minimum - Maximum-0.5293036 - 1.2025517
Average (Standard dev.)-0.00090786885 (±0.06338021)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-299-299-299
Dimensions600600600
Spacing600600600
CellA=B=C: 489.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45162_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45162_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45162_half_map_2.map
Projections & Slices
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Histogram (log scale)

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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: Portal protein
    • Protein or peptide: Phage protein
    • Protein or peptide: Head-closure protein
    • Protein or peptide: gp119
    • Protein or peptide: gp40
    • Protein or peptide: Putative structural protein
    • Protein or peptide: gp127
    • Protein or peptide: Phage 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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 55.291785 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MADITETQES LPPFRMGEVG SLGLKVRSGR IYEEPRQALR FPESIKTFQL MMRDPSVAAS VNIIKMFVRK VNWRFVPPKG KEKDAKMIE RANFFNSLMN DMEHDWADFI NSVMSFCTYG FCVNEKVYKK RQGKKGKYPS KYNDGLIGWA KLPIRNQTTL D KWYFDSDY ...String:
MADITETQES LPPFRMGEVG SLGLKVRSGR IYEEPRQALR FPESIKTFQL MMRDPSVAAS VNIIKMFVRK VNWRFVPPKG KEKDAKMIE RANFFNSLMN DMEHDWADFI NSVMSFCTYG FCVNEKVYKK RQGKKGKYPS KYNDGLIGWA KLPIRNQTTL D KWYFDSDY RKVIGVRQNL RNVSHTAGAI NLGEQPLTRK LPRSKFLLFK YDDEYGNPEG RSPLLNAYVP WKYKVQIEEF EA VGVSRDL VGMPKIGLPP DYLGEDAEPE KKAFVKYCQE VVNDLIANDR AGLIWPRFID PETKEDIFEF SLVSRQGAKA YDT GSIIDR YSKQIMMAFM SDVLAMGQSK YGSFSLADSK TSLLAMSVDI LLKQIKNVIN RDLVAQTYAL NMWDDEEHVE IVYD DIETP DIESIGSYVQ KTVAVGAMEV DKALSDKLRE HIGLEPADES KPVSENLSPN TQSRSGDGYQ TAGEGTAKTP SAKDP STAN KANK

UniProtKB: Putative portal protein

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Macromolecule #2: Phage protein

MacromoleculeName: Phage protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 17.058289 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString:
MCYTGDPANN PLDRVRILCT DTDNNEILID QSVLEWFYQE SGKDEKKAAI KALKYLLFQV AKMGDEKVGG VYLRNSSRFK SLKAVYDDL VKSSVSGLPY AGGINQCDID MRRQNPCSVK KYTEYGDAVR YYGRDYCERV NGVFIIERDE

UniProtKB: Phage protein

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Macromolecule #3: Head-closure protein

MacromoleculeName: Head-closure protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 15.467466 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString:
MRLLNRHSFV VKRKVSEDGH YNEDGDWVAS QDVVSINCKG NIQPYIKGSV KNGTQIVLPE GIRLTDTRIL FTVAELRTSD DVDWTEADI VMIKGHEYEV FMTMDWSEQL AHTSHYEYII IRRDKMNAVR NSRT

UniProtKB: Head-closure protein

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Macromolecule #4: gp119

MacromoleculeName: gp119 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 22.314221 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MQLETAELEK GIVRVLVDVI GHRLARDKNN RPNVIRAYPS DNSNDKGLKP DQPFITVYCQ DATTPYGWVL DKFVEDDAVC YRIAFQIPV LITVNGKGAH SIMLELKQRL EMSTTRDYLA DMTGASVLDT GAIPNDYTYL NTDFENSAPL VVTLVKNSVL K DERGSIIE ...String:
MQLETAELEK GIVRVLVDVI GHRLARDKNN RPNVIRAYPS DNSNDKGLKP DQPFITVYCQ DATTPYGWVL DKFVEDDAVC YRIAFQIPV LITVNGKGAH SIMLELKQRL EMSTTRDYLA DMTGASVLDT GAIPNDYTYL NTDFENSAPL VVTLVKNSVL K DERGSIIE RVIVDGELVY EEGQEPPEYT IHLDVDSKGV K

UniProtKB: Phage neck terminator protein gp12-like domain-containing protein

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Macromolecule #5: gp40

MacromoleculeName: gp40 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 16.204168 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString:
MAMYQQYSPK DVVCSWNGIA IEGFAPDSFL RLQRTSPLVT PVVGAGGQVA LTRNADKTGT IEIELMQTSL SNQMLSAIQA KQDDMELEE DISSNFVIYD PSGSVLATGI NAWLQELPQI ELGRDQNSKT WIFGCEKLDY TSTIPASSV

UniProtKB: Uncharacterized protein

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Macromolecule #6: Putative structural protein

MacromoleculeName: Putative structural protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 48.83477 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MWNPIVNVDI TLNTAGTTRE GFGLPLFLAS TDNFEERIRG YTSLTEVAED FDESTAAYKA AKQLWSQTPK VTQLYIGRRT MQYTVSIPD TVAEGSEYSL TVAIGGGVSQ PFQYTAKEND TALIVLNEFK SQIEASPTIK DGVNASVTGT GASATMIITK A GDNDFVKV ...String:
MWNPIVNVDI TLNTAGTTRE GFGLPLFLAS TDNFEERIRG YTSLTEVAED FDESTAAYKA AKQLWSQTPK VTQLYIGRRT MQYTVSIPD TVAEGSEYSL TVAIGGGVSQ PFQYTAKEND TALIVLNEFK SQIEASPTIK DGVNASVTGT GASATMIITK A GDNDFVKV TSITPTTSIA ATTADTASAA LASIETYSTD WYFISAEDRT QQFVLAMASE IQARKKIFFT ANADVKALQG TD LTSATDV PAQLAKSKYT RTVCLWHHTA EFDYPEMAYI AYGAPYDAGS IAWGNAQLTG VAASLQPANQ RPLISIQKSA LDT RSCNFI DLDGGVPVVR RGITSGGEWI DIVRGVDWLE SDLKTSLRDL LINQKGGKIT YDDTGITRIR QVIETSLQRA VNRK FLSTY TVTVPKASQV ALADKKARIL KDITFHGILA GAILDVDLKG TVAYE

UniProtKB: Putative structural protein

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Macromolecule #7: gp127

MacromoleculeName: gp127 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 18.445977 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString:
MAEVISISNA TRVHSYRGVL IITDELTVEA GSRVSLSGYV SDGGTSDVFT ICRLLDAPMN GKQFISNNCN EIVKIPFDSS CLLGVKLYN CENKRVNVNS VEAAFITIDT AFQSPMTVNK ESNRLEYIFS QNDYKVLVKG KVYDMIVNVV DESGNHSTIL K QKVRFN

UniProtKB: Uncharacterized protein

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Macromolecule #8: Phage protein

MacromoleculeName: Phage protein / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 11.613982 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString:
MGTLTIDGKN KILATLTPTT IVLHNVDPTA DPTANKVTQP VAIFFSEPNN GLIASEDTVN ITVPASATVS HFSLWDDNSK CVATGALSS PQFFAEEGIY VISSVSIDLN K

UniProtKB: Phage 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
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37006
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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