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- EMDB-46624: Shigella flexneri bacteriophage Moo19 Gp82 -

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Basic information

Entry
Database: EMDB / ID: EMD-46624
TitleShigella flexneri bacteriophage Moo19 Gp82
Map data
Sample
  • Virus: Shigella virus Moo19
    • Protein or peptide: Tail fiber protein
KeywordsMoo19 / Gp82 / VIRAL PROTEIN
Function / homologyTail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Tail fiber protein
Function and homology information
Biological speciesShigella virus Moo19
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_46624.png

Downloads & links

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Map

FileDownload / File: emd_46624.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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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-0.4617705 - 1.0368439
Average (Standard dev.)-0.00010187926 (±0.014627082)
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_46624_msk_1.map
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Half map: #1

Fileemd_46624_half_map_1.map
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Half map: #2

Fileemd_46624_half_map_2.map
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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: Tail fiber 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: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella virus Moo19
Molecular weightTheoretical: 118.004133 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGMNSHIPFD ADNDWTLDPY HCNRSNDPLV DKVIGNAYAV VRAVYCNLGN LKLLYDFLNT YGMVLGVKSE AELKKLNKLA KYARVYGFA DTGDRQVTDY LYVPDDTSGI RPDDQTATGS WIKVSTSGSG SGGTGGGSGS YIPYVYANGS ALGGETSFKV P AEALGVPF ...String:
MGMNSHIPFD ADNDWTLDPY HCNRSNDPLV DKVIGNAYAV VRAVYCNLGN LKLLYDFLNT YGMVLGVKSE AELKKLNKLA KYARVYGFA DTGDRQVTDY LYVPDDTSGI RPDDQTATGS WIKVSTSGSG SGGTGGGSGS YIPYVYANGS ALGGETSFKV P AEALGVPF IIINGSVQYI GYGFSFNPAN STVTLSNPLV QGDEVIALTS AAPASPDNPN VSNWVQVNWL YNNGAAVGGE QV ITVPYNF KDVPAVYKNG ERYYKNLQTK SYVYDPSTRT VTMTELLAQG DRVIITLGGE SASLEITDRT TQEVARANNV KDT DVVLSS STNVVITDKK VLYDVNAQKY WDLPNLPPNV YIVKVEGNKL IYNPGAVVID LLEPANPLVI VEPVLSRLGA ETGN PMAGT FEKGATVDSA AKSVGSTMEG KLYRWEGALP KTVRAGDTPS SSGGIGSGKW VEITNATLRS QLASTGGAAM VKASD GRTV EQWLVQSDSA SFRAKNMAKL AWCDYQVHNR GSLKCCFLGD SMTAGFDRTS SDTIPAQDGD WATRASMNYP YRFASY LPE QSGCSVYITM RAISGYTAKQ AYEEALWQSN PNCDIVFIMY AINDSGGVAG ATLDLYMEYM EKLIRRYIDW GCAVVVQ RP SGGGQGAGNP AWLHWAKRMQ MVARVYGCPV FDAHEVMLNR HYAAVQSDGT HYNSMGYAIH GEKLASMLMA GGLLDTYK P VVNETTVWTG MMSDHIGWCD ARGNIGTGRS DGAYTRDKVT GVLQAGKATI CTFSFYLDAE AAHIYGKLDG LINTIYTNG YWWNNGNKPY YQYAVDIDNS FGASLQRVNK SANNYEGMPG SRKFVGRLIG RGWHTITLFT NLQGEALKDA FVNSITVQPI PIGLSTEQM WGQDEERRYR VVHTRRMPSP SGQGGTLPVA VALTGFQMRA PQSFLGTGPG TNAVPAPYFY NTVPGKLKVY N EKGDYIEW LVYKDGSSGL KWKGKVLTHS FADVASVPTL TAYMGTAKQN VIVAAGSSGA NQPLENIYDY NAGLQEQTGN PS TDLSWKG GIYLVFTLAW PSTAPTGYWT IELEGSDWFG NSESAVGCF

UniProtKB: Tail fiber 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 TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 43.0 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 / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 563035
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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