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- EMDB-46623: Shigella flexneri bacteriophage Moo19 Tail -

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Basic information

Entry
Database: EMDB / ID: EMD-46623
TitleShigella flexneri bacteriophage Moo19 Tail
Map data
Sample
  • Virus: Shigella virus Moo19
    • Protein or peptide: Portal protein
    • Protein or peptide: Gp83
    • Protein or peptide: Tail protein
    • Protein or peptide: Tail fiber protein
KeywordsMoo19 / VIRUS
Function / homology
Function and homology information


: / Phage SU10 portal protein / Tail 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
Similarity search - Domain/homology
Tail protein / Portal protein / Tail fiber protein / Uncharacterized protein
Similarity search - Component
Biological speciesShigella virus Moo19
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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_46623.png

Downloads & links

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Map

FileDownload / File: emd_46623.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 500 pix.
= 816. Å		1.63 Å/pix.
x 500 pix.
= 816. Å		1.63 Å/pix.
x 500 pix.
= 816. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.16805108 - 0.23100673
Average (Standard dev.)0.0002709482 (±0.00409319)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-249-249-249
Dimensions500500500
Spacing500500500
CellA=B=C: 816.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46623_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46623_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46623_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: Portal protein
    • Protein or peptide: Gp83
    • Protein or peptide: Tail protein
    • 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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella virus Moo19
Molecular weightTheoretical: 85.342766 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MEHQDSMTPL PDPGQSDKLT NWKKEPSIQT LKADLEAGKP AHDAIMKEIQ KWNDLMKAEG SAKPPKVKGR SQVQPKLVRR QAEWRYAPL SEPFLSSPKL FKLTPVTWED EQAARQNELV LNYQFRTQLN RVKLVDDYVH SVCDDGTGIA RVGWERKVVK V KQDAPVFQ ...String:
MEHQDSMTPL PDPGQSDKLT NWKKEPSIQT LKADLEAGKP AHDAIMKEIQ KWNDLMKAEG SAKPPKVKGR SQVQPKLVRR QAEWRYAPL SEPFLSSPKL FKLTPVTWED EQAARQNELV LNYQFRTQLN RVKLVDDYVH SVCDDGTGIA RVGWERKVVK V KQDAPVFQ MYPVETEEQV QILQQALDLQ AQNPRGYEEQ VADDVKEAVN YFNETGEATY AIQTGTTEVE VEKAVVNRPT VE MLDPNNV VIDPSCNGDL DRALFAVVSF ETCKADLLKT PDRYHNLDKI DWESSSPLTD PDHESKTPGD FQFRDAMRKR VIA YEYWGF WDTNGDGELK PIVATWIGTT LIRMEENPYP DGKLPFVLVP YMPRKRELYG EADAELLGDN QKILGATMRG MIDL LGRSA NGQRAYPKGM LDTLNRRRFE DGLDYEYNPQ TGNPSQAIIE HKFPELPQSA IVMSQMQNQE AEALTGVKAF AGGVT GSAY GDVAAGIRGA LDAASKREMA ILRRLAKGMA DIGTKICAMN AVFLSETEVV RITNEEYVTI NREDLKGNFD IEVDIN TAE VDNQKSQDLG FMVQTIGNTV DQQVTLKLVA RIAELKRMPE LAHELRTWKP EPDPMEEQLK QLAIQKAQLE NQKLQSE IA LNEAKVRAED AKKDMTNLDY LEQESGTKHA REMEKQKAQS QGNQNLQVTK ALTQPVKEGE TSPNISAAIG YNAITDGN N QVNNELERDA LAPQDPSLSI GSQYFDPSRD PALSPGMNL

UniProtKB: Portal protein

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Macromolecule #2: Gp83

MacromoleculeName: Gp83 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella virus Moo19
Molecular weightTheoretical: 26.990467 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MRKLSDVYKV LALTSLKSAG FITDDKVNIE AWGKPEVLAH INEGLTRLHS RFVLRTNNCI VEMKEGRTDY PLLARYSYER FDPAKAPYP YIMDTPQEPF QEDVIKILNV YDSKGIRRKL NDDHDKNGLF TPRPDVLQCM WPRHFEALNV LYQAKHPELT G DENQEIDL ...String:
MRKLSDVYKV LALTSLKSAG FITDDKVNIE AWGKPEVLAH INEGLTRLHS RFVLRTNNCI VEMKEGRTDY PLLARYSYER FDPAKAPYP YIMDTPQEPF QEDVIKILNV YDSKGIRRKL NDDHDKNGLF TPRPDVLQCM WPRHFEALNV LYQAKHPELT G DENQEIDL PETLYSALEN WVGYRYHTGL NTEGSTAKAA EYLQLYESIC GEVVDFDLAN GSMSNTNVLF EKRGWV

UniProtKB: Uncharacterized protein

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Macromolecule #3: Tail protein

MacromoleculeName: Tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella virus Moo19
Molecular weightTheoretical: 30.295928 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (bacteria)
SequenceString: MSCGAEVEAN RLLLALTEGE DFALPDIDMS GPEWDIPGGD GSPIFAEVTR LTNEDLTTRV VGGSGTFDAL MASAAAHLKQ EFKEGRITG GEYTKAYIAI VETCMGNATQ YLLGRDQAYW AAAMAQIQAV SARVALATSK AQYVLAKFQA LNAKSEYALT K LKLSTESE ...String:
MSCGAEVEAN RLLLALTEGE DFALPDIDMS GPEWDIPGGD GSPIFAEVTR LTNEDLTTRV VGGSGTFDAL MASAAAHLKQ EFKEGRITG GEYTKAYIAI VETCMGNATQ YLLGRDQAYW AAAMAQIQAV SARVALATSK AQYVLAKFQA LNAKSEYALT K LKLSTESE TYCAALFNVE QTLPQQLKLL IEQTEAQRAQ TLDKRSDGAT VSGSIGKQKE LYTQQITSYQ RDAEVKASKL FT DAWITQK TIDEGLTPPN GFTNSSIDDV LTTLKRNNNL NG

UniProtKB: Tail protein

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Macromolecule #4: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shigella virus Moo19
Molecular weightTheoretical: 118.004133 KDa
Recombinant expressionOrganism: Shigella flexneri 2a str. 2457T (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 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: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 95783
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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