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- EMDB-46622: Shigella flexneri bacteriophage Moo19 Icosahedral Reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-46622
TitleShigella flexneri bacteriophage Moo19 Icosahedral Reconstruction
Map data
Sample
  • Virus: Shigella virus Moo19
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Ig-like domain-containing protein
KeywordsMoo19 / VIRUS
Function / homologyPhage capsid protein / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Ig-like domain-containing protein / Major capsid protein
Function and homology information
Biological speciesShigella virus Moo19
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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_46622.png

Downloads & links

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Map

FileDownload / File: emd_46622.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 800 pix.
= 1305.6 Å		1.63 Å/pix.
x 800 pix.
= 1305.6 Å		1.63 Å/pix.
x 800 pix.
= 1305.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.15321209 - 0.24061404
Average (Standard dev.)0.0008289848 (±0.0075159417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 1305.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46622_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_46622_half_map_1.map
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Half map: #2

Fileemd_46622_half_map_2.map
Projections & Slices
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Sample components

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Entire : Shigella virus Moo19

EntireName: Shigella virus Moo19
Components
  • Virus: Shigella virus Moo19
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Ig-like domain-containing protein

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Supramolecule #1: Shigella virus Moo19

SupramoleculeName: Shigella virus Moo19 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2886042 / Sci species name: Shigella virus Moo19 / 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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Shigella virus Moo19
Molecular weightTheoretical: 43.971672 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MLNYNAPIDG QKSSIDGAGS DQMNTFYWLK KAIIQARKDQ YFMPLASVTN MPKNMGKTIK VYEYVPLLDD RNINDQGIDA NGAHIVNGN LYGSSKDIGT ITSKLPLLTE NGGRVNRVGF TRLSREGSIH KFGFFYEFTQ ESLDFDSDDQ LKEHLSRELM N GAVQITEA ...String:
MLNYNAPIDG QKSSIDGAGS DQMNTFYWLK KAIIQARKDQ YFMPLASVTN MPKNMGKTIK VYEYVPLLDD RNINDQGIDA NGAHIVNGN LYGSSKDIGT ITSKLPLLTE NGGRVNRVGF TRLSREGSIH KFGFFYEFTQ ESLDFDSDDQ LKEHLSRELM N GAVQITEA VLQKDLLAAA GTVLYAGAAT SDATITGEGS TPSVITYKNL MRLDAILTDN RTPTQTTIIT GSRLVDTKVI GG TRVMYVG SELVPDLKAM KDLFGNKAFI EIQHYGDAGT LMNGEIGTID KFRIIQVPEM LHWAGAGAAA TDANPGYRTS TVN GTEHYD VYPVLVVGDD SFTTIGFQTD GKSVKFNVMT KMPGKETADR NDPYGETGFS SIKWYYGILV KRPERIAVMK AVAP L

UniProtKB: Major capsid protein

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Macromolecule #2: Ig-like domain-containing protein

MacromoleculeName: Ig-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shigella virus Moo19
Molecular weightTheoretical: 28.133709 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MPELKVAFNK DTYVATVLDA SGSVPSGSVN VGTFFHPDET YPDSYVIYHG VRELLYKRSE VDPAQPGFWP ENITNMQAVT IDNKATARL VLNTSLPRVV STIEGGKVTL SVVALGGKAP LKYKWEFRAP NASTWTAVSG QTTANLVLDN IDADKAGEYK V TVTDAAGT ...String:
MPELKVAFNK DTYVATVLDA SGSVPSGSVN VGTFFHPDET YPDSYVIYHG VRELLYKRSE VDPAQPGFWP ENITNMQAVT IDNKATARL VLNTSLPRVV STIEGGKVTL SVVALGGKAP LKYKWEFRAP NASTWTAVSG QTTANLVLDN IDADKAGEYK V TVTDAAGT SVDSTALVAV GAYPPPALTG IKATPTSLSL SVATDAAGKT VALSAIPTDA ELGTLSIKTA PDSARATATI SG STLTVKP VAAGAATSVV VTNGKVDVTI TINVAA

UniProtKB: Ig-like domain-containing 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:
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: 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

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 99582
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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