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- EMDB-46626: Shigella flexneri bacteriophage B2 Icosahedral Reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-46626
TitleShigella flexneri bacteriophage B2 Icosahedral Reconstruction
Map data
Sample
  • Virus: Shigella phage B2 (virus)
    • Protein or peptide: B2 Capsid
    • Protein or peptide: B2 Dec Gp45
KeywordsB2 / VIRUS
Biological speciesShigella phage B2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_46626.png

Downloads & links

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Map

FileDownload / File: emd_46626.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 800 pix.
= 1334.4 Å		1.67 Å/pix.
x 800 pix.
= 1334.4 Å		1.67 Å/pix.
x 800 pix.
= 1334.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.019736048 - 0.06374727
Average (Standard dev.)0.0005358853 (±0.0028223316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-399-399-399
Dimensions800800800
Spacing800800800
CellA=B=C: 1334.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46626_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_46626_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46626_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: B2 Capsid
    • Protein or peptide: B2 Dec Gp45

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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: B2 Capsid

MacromoleculeName: B2 Capsid / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 42.530359 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MKYNAPNTTP SSIGPQIRLD YYYKKALVDA AKEMYFGQLA EVTNMPKNMG KQIKLYHYVP LLDDRNVNDQ GIDAAGATIA NGNLYGSSK DIGTIPSKLP ALTENGGRVN RVGFTRIQLI GSIKKFGFFY EWTQEAMDFD TDEELDSHLI QEAVKGANEI T EDQLQIDL ...String:
MKYNAPNTTP SSIGPQIRLD YYYKKALVDA AKEMYFGQLA EVTNMPKNMG KQIKLYHYVP LLDDRNVNDQ GIDAAGATIA NGNLYGSSK DIGTIPSKLP ALTENGGRVN RVGFTRIQLI GSIKKFGFFY EWTQEAMDFD TDEELDSHLI QEAVKGANEI T EDQLQIDL LNGAGVVRYP GAATSNADMT GEGTATVVTY EGLVKMGITL NDNLCPMQTK LIAGSLMTDT RTIQGARALY IG SELELQL RKMKDPFDNA AFIPVQQYAD AGNLLKGEIG SIASFRVIVV PKMLKWAGAG ATVTTNPGYY ATSGKYDVFP MLC VGSGSF TTIGFQTDGK TVKFTTYTKK PGIETVSYAD PYGEMGLTSI KWYYGSLILR PEWIALFKTV AAM

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Macromolecule #2: B2 Dec Gp45

MacromoleculeName: B2 Dec Gp45 / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage B2 (virus)
Molecular weightTheoretical: 9.495771 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString:
MAYSDVDAIL ADGKQAVAVK HGGGLVVVGE LGAQVLAAKD VSELPDGVGG TAPGAATTTT AGVVKQSTTQ AASVATDVAG VVTDLNALI TKLKAAGIMA

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135384
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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