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- EMDB-46628: Shigella flexneri bacteriophage B2 Gp48 and Gp49 -

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Basic information

Entry
Database: EMDB / ID: EMD-46628
TitleShigella flexneri bacteriophage B2 Gp48 and Gp49
Map data
Sample
  • Virus: Shigella phage B2 (virus)
    • Protein or peptide: Gp48
    • Protein or peptide: Gp49
KeywordsB2 / Gp48 & Gp49 / VIRAL PROTEIN
Biological speciesShigella phage B2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsSubramanian S / Bergland Drarvik SM / Parent KN
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
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: Sci Adv / Year: 2024
Title: Moo19 and B2: Structures of podophages with = 9 geometry and tailspikes with esterase activity.
Authors: Sundharraman Subramanian / Silje M Bergland Drarvik / Kendal R Tinney / Sarah M Doore / Kristin N Parent /
Abstract: Podophages are, by far, the least well studied of all the bacteriophages. Despite being classified together due to their short, noncontractile tails, there is a huge amount of diversity among members ...Podophages are, by far, the least well studied of all the bacteriophages. Despite being classified together due to their short, noncontractile tails, there is a huge amount of diversity among members of this group. Of the podophages, the N4-like family is the least well studied structurally and is quite divergent from well-characterized podophages such as T7 and P22. In this work, we isolate and fully characterize two members of the family by cryo-electron microscopy, genetics, and biochemistry. We describe the capsid features of Moo19 and B2, including a decoration protein. In addition, we have fully modeled the tail machinery for both phages and identify proteins with esterase activity. Genetic knockouts of the host reveal factors specific for host attachment including key modifications to the O-antigen on the lipopolysaccharide. Moo19 and B2 are both members, yet some distinct differences in the genome and structure place them into distinct clades.
History
DepositionAug 18, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46628.png

Downloads & links

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Map

FileDownload / File: emd_46628.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 560 pix.
= 496.16 Å		0.89 Å/pix.
x 560 pix.
= 496.16 Å		0.89 Å/pix.
x 560 pix.
= 496.16 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.886 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.5239718 - 1.1559917
Average (Standard dev.)-0.0002866882 (±0.014305919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-279-279-279
Dimensions560560560
Spacing560560560
CellA=B=C: 496.15997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46628_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_46628_half_map_1.map
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Half map: #1

Fileemd_46628_half_map_2.map
Projections & Slices
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Sample components

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Entire : Shigella phage B2

EntireName: Shigella phage B2 (virus)
Components
  • Virus: Shigella phage B2 (virus)
    • Protein or peptide: Gp48
    • Protein or peptide: Gp49

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Supramolecule #1: Shigella phage B2

SupramoleculeName: Shigella phage B2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2968270 / Sci species name: Shigella phage B2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri 2a str. 2457T (bacteria)

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Macromolecule #1: Gp48

MacromoleculeName: Gp48 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 83.297094 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNQLFSQGGK GSAGILTNKQ AVARHFGVKQ SEVVYFSVGV DISGYKVIYD KTTQRAYSLP IGIPAGTTAI SLSTAAVLVH SQGSVDLGA VAVLRKEYVT IPGDFTSGAT IQVKNEILTH SNGAQYRWAG AVPKVVPAGS TPASSGGISA SAWIEVTGEE L RDELATTG ...String:
MNQLFSQGGK GSAGILTNKQ AVARHFGVKQ SEVVYFSVGV DISGYKVIYD KTTQRAYSLP IGIPAGTTAI SLSTAAVLVH SQGSVDLGA VAVLRKEYVT IPGDFTSGAT IQVKNEILTH SNGAQYRWAG AVPKVVPAGS TPASSGGISA SAWIEVTGEE L RDELATTG GASQIGTSDG KTVQQWIIAN DSANYRARNI QKLAWVDKQV HSRGSIKVLF QGDSMTAGYD TTSTDRVPAN NG DWATHAS MTYPQRFMAY LPEQSGCSVT GVYRAISGHT AIQSYNEPSW QSNPNCDVVI LMLGLNDAGG VAGTTEDIYM EYM EKLIRR FIDWGMGVVV QTCSTGGQGS GGVVANLWAK RMRMMADTYG CAHFNADEVQ YYRHNGAVQS DGGHFNSMGY AIHG QMLAS MFMAGGLLPT YRPLTNEINT WCGRLDDSIG YCDATGNINL GRSDGAYTRT KVVGGMLANV ASIATFSFYL DAEAA HIFV HGSGAGPINV LVDAPSWWNN GAQDYYDFAN NQSINFSNSP QAANNAIVDL STTYSADRKF VGRILGRGWK TLTFFT NLQ GTGGDFYLNS LTVQPVPVGM SVQARNWARF DKGHRAVYSK KIPQAYNQAT LPTATALVNF QVPMPQSMLP TTPSISG DL GTNFYNCGHS VLKISNSSGD YLEVLLIKTT GGGYVFTGKI LKTTYATGNQ PTAITATAAH YSMKDLKVAG ANGPNMPL E TIRDIDMASY VTIGVGAGNG GLVLDINITW PSTPPTSYWN IELEAWDMFG NSEASI

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Macromolecule #2: Gp49

MacromoleculeName: Gp49 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 44.471602 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIRTTNTCCG NQAGMVEKFI GTAYDVVKTV YDNLGEIQFI YNFLNDYGVL ITVDSVTELQ ELPTTAKYTR VYSSTPTGVR IYTDYLYVE GDRTGVLPSD PTATGSWVVV GSSNSGAATG TGAYIPFVFN NGSAAGGETT IVVPDYTIGV PEIYVEGFRQ Q VGRGFTFN ...String:
MIRTTNTCCG NQAGMVEKFI GTAYDVVKTV YDNLGEIQFI YNFLNDYGVL ITVDSVTELQ ELPTTAKYTR VYSSTPTGVR IYTDYLYVE GDRTGVLPSD PTATGSWVVV GSSNSGAATG TGAYIPFVFN NGSAAGGETT IVVPDYTIGV PEIYVEGFRQ Q VGRGFTFN SVNLTVTLAQ PLEQGDEVVL MLSGNPAVPD NPNIDSWTVI NWIYNNGAAV GGEQVIVIPY TFQTVPAIFK NG LRYQGGL STQSYTVDQD NKRILLTEPL STNDRLVVQL GGELVTLESP DRSLYEIARA TNMKDSEVIK SDNTVETLNG KRI LYDIVS QVYYWIPSSV PNNVYIQSVV NGQLTYLPGN IVVTLTPIVT LGLSGTTAQR PIGVLTGTQH FDTTLGKPIW FNGT AWVDS TGAVV

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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:
ConcentrationNameFormula
10.0 mMtris(hydroxymethyl)aminomethane
10.0 mMmagnesium chlorideMgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 43.14 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2078531
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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