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- EMDB-70310: Sf11 bacteriophage tail -

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Basic information

Entry
Database: EMDB / ID: EMD-70310
TitleSf11 bacteriophage tail
Map data
Sample
  • Virus: Shigella phage Sf11 SMD-2017 (virus)
    • Protein or peptide: Putative neck whiskers protein gp24
    • Protein or peptide: Tail fiber protein gp17
    • Protein or peptide: Putative tail protein gp14
    • Protein or peptide: gp16
    • Protein or peptide: Putative tail protein gp13
    • Protein or peptide: Tail tape measure protein gp18
KeywordsSf11 / bacteriophage / VIRUS
Function / homology
Function and homology information


viral tail assembly
Similarity search - Function
Tape measure protein N-terminal / Tape measure protein / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative tail protein / Tail tape measure protein / Tail fiber protein / Putative neck whiskers protein / Putative tail protein / Uncharacterized protein
Similarity search - Component
Biological speciesShigella phage Sf11 SMD-2017 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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_70310.png

Downloads & links

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Map

FileDownload / File: emd_70310.map.gz / Format: CCP4 / Size: 1.4 GB / 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 720 pix.
= 600.48 Å		0.83 Å/pix.
x 720 pix.
= 600.48 Å		0.83 Å/pix.
x 720 pix.
= 600.48 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: 0.15
Minimum - Maximum-0.4788131 - 0.8747548
Average (Standard dev.)-0.00017225771 (±0.023219638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-360-360-360
Dimensions720720720
Spacing720720720
CellA=B=C: 600.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70310_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70310_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_70310_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: Putative neck whiskers protein gp24
    • Protein or peptide: Tail fiber protein gp17
    • Protein or peptide: Putative tail protein gp14
    • Protein or peptide: gp16
    • Protein or peptide: Putative tail protein gp13
    • Protein or peptide: Tail tape measure protein gp18

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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: Putative neck whiskers protein gp24

MacromoleculeName: Putative neck whiskers protein gp24 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 25.037666 KDa
SequenceString: MAICANDKGV LVGRMTRLFL AEGCGDAVPD AGDWKYLGST TSKGVDYSPQ TTTSEADTAG GFVSTLVTSS DMTISAEVEI RKNDPSDEF GFHRLVEIYA TELKARRQPS LWVRQVTGAT IVTAYCNITS ISYEGGTNDI VTGSLEFKVY DSDSVTVESL E PLAFTTDL ...String:
MAICANDKGV LVGRMTRLFL AEGCGDAVPD AGDWKYLGST TSKGVDYSPQ TTTSEADTAG GFVSTLVTSS DMTISAEVEI RKNDPSDEF GFHRLVEIYA TELKARRQPS LWVRQVTGAT IVTAYCNITS ISYEGGTNDI VTGSLEFKVY DSDSVTVESL E PLAFTTDL QSTGSTGTPL TVAVEGGVAP YTYVWRKDGV VVGSESGATL ASPTAGVYTV TVTDSSTDPE VIISTACTVS

UniProtKB: Putative neck whiskers protein

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Macromolecule #2: Tail fiber protein gp17

MacromoleculeName: Tail fiber protein gp17 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 50.176445 KDa
SequenceString: MAIIKYPDWI PLAQRASKNL TQQTPFRSDQ PAVGAPIFQK LTTDIVATWS LTWVFTLAEE RAFIQWLRSS RYLNKCNNWF TMMIDLGGS GLQEQTLHFT DYPVQTSIDG GVVTWTGNVI AKKLNNTMDE FDDVLVELDY RWYGWLDEVV NRELPQVYMT P ILHMPINM ...String:
MAIIKYPDWI PLAQRASKNL TQQTPFRSDQ PAVGAPIFQK LTTDIVATWS LTWVFTLAEE RAFIQWLRSS RYLNKCNNWF TMMIDLGGS GLQEQTLHFT DYPVQTSIDG GVVTWTGNVI AKKLNNTMDE FDDVLVELDY RWYGWLDEVV NRELPQVYMT P ILHMPINM LSSTLDSRIV YDGPQVYYIN RNGNLVQSAA NEWPLTFIDG VAVGRVPPEN TSKNVILYNT NLTNVVWART RM SITPSPQ TGMLVNGCFK LTPTTDSNTH LVAQLPVFEI LEGEVCTFSV IAKADGYRNV RIRIANNAVF VADVTVNLLS GVI IGGSAN SSIENLGGGW FRFSEIVTPT EGGYSAIAMQ IWVHDDSNSA TFAGDGVSGI LVCAPQSDST GASMSPIATE ASPV TRPTA SAKVVMNGAT SIDITYSDSS TINVPAVDNY AVIPQADSAW GSKYITTIKF NV

UniProtKB: Tail fiber protein

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Macromolecule #3: Putative tail protein gp14

MacromoleculeName: Putative tail protein gp14 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 92.301906 KDa
SequenceString: MPVIHVQKMP GTPKETGIVP AGTNLWKWLN KSNLPASISI TVNGRVLGED DELSFCLRDG DVVNVYCQPS GAIGDLIGAI LKPVTKIFS FLTPKVSTPK TDTSSKTSPN TSLKAQTNIA RNGEARPDNF GQIRAFPDLL QESLFEYINN IKYVTEFMNF G LGKYDVSS ...String:
MPVIHVQKMP GTPKETGIVP AGTNLWKWLN KSNLPASISI TVNGRVLGED DELSFCLRDG DVVNVYCQPS GAIGDLIGAI LKPVTKIFS FLTPKVSTPK TDTSSKTSPN TSLKAQTNIA RNGEARPDNF GQIRAFPDLL QESLFEYINN IKYVTEFMNF G LGKYDVSS VRYSESNLGS LAGASYTIYQ PGEVIPVVYE PYAFDDVDGQ ELYGPNELDT DPPPVVIETA TTTTVTETEF AG GQIAVKI PKDPAFNYFV DLTMPHDVVF KLNITYAQGG GASVTENVTL SGRLVSATET DDGGLPPANY WYTFIINSIN YSG APISSL SGVTINNTYF NLTDNQPIVS GPYFSPIDGD QLWVHLQHQT NDGNDFSVLI EWWKIDDDNV QIPGTYQSMN YYRD VDRND TFYYTIKLTP SAGTGRYAIQ MRRTNNSSDT SILQLEEIHS IVTRTNVSYS DDTVVKVVVR ATENATGSRD RKYNA LITR HTIGYNRDAG TVRYTLAPSR SFADAVLHNW LITAGNPENT IDIVRLYEIA DSLPDERLGY FDYTFDDEDK SIGERL QTI CDAARVTAFW DDGVMSFSRD EKRDYPATVF NTRNTQSDGY KLSYDISLPG TYDGVNVEYR DPTTNKQANV YYRITDS GI VEGEPTKAKK FDMLYVRNRY QAVDRAILEC RRLIYSRRSM EIKALADGEW VNVGDMIQVV DMYDDVQQTG VIEARNGN T FTTSEQLTAD DNLYVVITSS DGSVSGRLPA TVTGLHTFTC NLPSDFQLNI WDGTSVQSES RYVLSTEKEL DTTLWVVSQ KNPGSDGTTT LTMSEYSDEM YEYVISSS

UniProtKB: Putative tail protein

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Macromolecule #4: gp16

MacromoleculeName: gp16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 17.654084 KDa
SequenceString:
MPSLRDYKAK RPNWALFDTI TFYHSSFGYV RLVANVLDEM VLGGETYSPV RMDITQSQQS NTPAINATVK FARLANDFKQ YLKLWTGSG RIEPISALYQ RFEETDTNTP LKPYRLYVSD VAMDGSDVTV ALSIKNPIKG NVAKLYDIAQ FPGLRNV

UniProtKB: Uncharacterized protein

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Macromolecule #5: Putative tail protein gp13

MacromoleculeName: Putative tail protein gp13 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 61.978992 KDa
SequenceString: MATVPTNNPI PSEDPRDLKF NAGKIDEVVN SDAHYYTDRF GKQRWTMAGF QKTTQDAIRS YGYITMDGFE DGATLTLPNQ VLRYEATGE YYRWDGDFPK TVSSGSTPET AGGVGSGAWL SVGDGSLRAD LSSTDDGRGC SLIGTSDGSN VQEALDDINN T IYQDPLTK ...String:
MATVPTNNPI PSEDPRDLKF NAGKIDEVVN SDAHYYTDRF GKQRWTMAGF QKTTQDAIRS YGYITMDGFE DGATLTLPNQ VLRYEATGE YYRWDGDFPK TVSSGSTPET AGGVGSGAWL SVGDGSLRAD LSSTDDGRGC SLIGTSDGSN VQEALDDINN T IYQDPLTK WPLGGTLKIK QGVYDVSSAL TLDYGNYDAT FIGSPGVRAH YVGENMAETI FNCQVADFNL KMLGDTVGAT QR VHAYDYL GNITLKGSAT SYGLLVTKKA YTKLENIVSY GHTNGEGLRT DSVLTAELDN VYLQSNRIGW RVLNTGDESE LNA ITVNRL TASQNTQWGI LGDRWGAGTT INSLTCEGNG TQGDSGTGGM QIAVNGLNGS CALVLNNPYF EANAGGSDLA IDNT GTRPV TVIINGGNFH RVSSTAYTVN NLSITSSGGG KVTVILNGTT FQSVGSYVPS SARPYWVTGA NCEVIDIGCT FMEQT SKAT SVSSGSIPRS GRINSNGSID VAPGVSSVNM VTTGVYDVTF SQQLSTSANG YVVQITPISA PDSVSCDVIY SSTTSF RVT LRNTVSGAGI ASAFAFSVTR LV

UniProtKB: Putative tail protein

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Macromolecule #6: Tail tape measure protein gp18

MacromoleculeName: Tail tape measure protein gp18 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf11 SMD-2017 (virus)
Molecular weightTheoretical: 82.248141 KDa
SequenceString: MAEEVGGIVY EVGMDVKGLK AGATTANKTL DDLESSLNKT TGEFNKLDKG ARNAGSGMKN AGGAASGLKT SMSMLAGAIS VSLIIEWGK RFLEVADNMT QLQARIARLS TDAKTANETF SSLANIASTT GASLSDTTKL WETLTSSLKE AGATNAQVLN L TDTLQKIG ...String:
MAEEVGGIVY EVGMDVKGLK AGATTANKTL DDLESSLNKT TGEFNKLDKG ARNAGSGMKN AGGAASGLKT SMSMLAGAIS VSLIIEWGK RFLEVADNMT QLQARIARLS TDAKTANETF SSLANIASTT GASLSDTTKL WETLTSSLKE AGATNAQVLN L TDTLQKIG RIGGSSTEEM ANALRQFGQS IASGTIRAEE FNSILEQMPE LARQIAAGLG ISMGELRARM LDGKLTAEDA LN AIQDRTS VVNAEFEKLP RTMDQAVGSL EVSFSKLVVA VNDATGASKT AVEIIDQLAK YIDFLGDKST STSDKILSLA TVI SKLNPG AWAQMGVDAL FGDDDIEKQK QYNDQVERFV KASAEGYEQT KKQAEATKHL KIAQAPTKDK KGKGKGKSAE ERQA ESVAE KLEKLRQQTM LNATSTGELS REQAILNAQQ SLGKAATQEQ IKLAGEYAAK IWDQKNALKE QAAAEKERID AVKGY SALK SKASPMFAVE TSYQKDMADL DAYAKAYPQK MAEIQQTRAT IEEQYRQQRM DAMWQEWSQQ NAATQAAAAA FDAFGQ TAG NALTGILTGS MSVSEALRSI GSNILSSVIN AFVQMGIQWA QSVIMGQAGM AAASAATIAQ AAAISAAMAP AAAMTSL AT AGTNSAPAMA GMSATVGLAK TLSIAGALKN GGPAQEGSMY RVGENNLPEI FQASNGHQYM IPGDSGRVIS NKDLTGGG G GVVVYNNVIN NSSAQVSSSA RDNGDGSVTI ETIISDIENN GPIGQSISRN YSANRRATE

UniProtKB: Tail tape measure 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: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35748
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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