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- EMDB-41649: P22 Mature Virion tail - C6 Localized Reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-41649
TitleP22 Mature Virion tail - C6 Localized Reconstruction
Map data
Sample
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Packaged DNA stabilization protein gp10
Keywordsphage / bacteriophage / tail spike protein / TSP / gene product 9 (gp9) / Packaged DNA stabilization protein / gene product 10 (gp10) / STRUCTURAL PROTEIN / VIRAL PROTEIN
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / metabolic process / virion attachment to host cell
Similarity search - Function
Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Tail spike protein / Packaged DNA stabilization protein gp10
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsIglesias S / Cingolani G / Feng-Hou C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM140733 United States
CitationJournal: J Mol Biol / Year: 2023
Title: Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery.
Authors: Stephano M Iglesias / Ravi K Lokareddy / Ruoyu Yang / Fenglin Li / Daniel P Yeggoni / Chun-Feng David Hou / Makayla N Leroux / Juliana R Cortines / Justin C Leavitt / Mary Bird / Sherwood R ...Authors: Stephano M Iglesias / Ravi K Lokareddy / Ruoyu Yang / Fenglin Li / Daniel P Yeggoni / Chun-Feng David Hou / Makayla N Leroux / Juliana R Cortines / Justin C Leavitt / Mary Bird / Sherwood R Casjens / Simon White / Carolyn M Teschke / Gino Cingolani /
Abstract: Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid ...Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid assembly. Here, we describe the complete architecture of the P22 tail apparatus (gp1, gp4, gp10, gp9, and gp26) and the potential location and organization of P22 ejection proteins (gp7, gp20, and gp16), determined using cryo-EM localized reconstruction, genetic knockouts, and biochemical analysis. We found that the tail apparatus exists in two equivalent conformations, rotated by ∼6° relative to the capsid. Portal protomers make unique contacts with coat subunits in both conformations, explaining the 12:5 symmetry mismatch. The tail assembles around the hexameric tail hub (gp10), which folds into an interrupted β-propeller characterized by an apical insertion domain. The tail hub connects proximally to the dodecameric portal protein and head-to-tail adapter (gp4), distally to the trimeric tail needle (gp26), and laterally to six trimeric tailspikes (gp9) that attach asymmetrically to gp10 insertion domain. Cryo-EM analysis of P22 mutants lacking the ejection proteins gp7 or gp20 and biochemical analysis of purified recombinant proteins suggest that gp7 and gp20 form a molecular complex associated with the tail apparatus via the portal protein barrel. We identified a putative signal transduction pathway from the tailspike to the tail needle, mediated by three flexible loops in the tail hub, that explains how lipopolysaccharide (LPS) is sufficient to trigger the ejection of the P22 DNA in vitro.
History
DepositionAug 18, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41649.png

Downloads & links

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Map

FileDownload / File: emd_41649.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.16582 Å
Density
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-27.985128 - 35.451756000000003
Average (Standard dev.)0.000000000001705 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 512.9599 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41649_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41649_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41649_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Salmonella phage P22

EntireName: Salmonella phage P22 (virus)
Components
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Packaged DNA stabilization protein gp10

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Supramolecule #1: Salmonella phage P22

SupramoleculeName: Salmonella phage P22 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2908168 / Sci species name: Salmonella phage P22 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica (bacteria)

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Macromolecule #1: Tail spike protein

MacromoleculeName: Tail spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 71.923523 KDa
SequenceString: MTDITANVVV SNPRPIFTES RSFKAVANGK IYIGQIDTDP VNPANQIPVY IENEDGSHVQ ITQPLIINAA GKIVYNGQLV KIVTVQGHS MAIYDANGSQ VDYIANVLKY DPDQYSIEAD KKFKYSVKLS DYPTLQDAAS AAVDGLLIDR DYNFYGGETV D FGGKVLTI ...String:
MTDITANVVV SNPRPIFTES RSFKAVANGK IYIGQIDTDP VNPANQIPVY IENEDGSHVQ ITQPLIINAA GKIVYNGQLV KIVTVQGHS MAIYDANGSQ VDYIANVLKY DPDQYSIEAD KKFKYSVKLS DYPTLQDAAS AAVDGLLIDR DYNFYGGETV D FGGKVLTI ECKAKFIGDG NLIFTKLGKG SRIAGVFMES TTTPWVIKPW TDDNQWLTDA AAVVATLKQS KTDGYQPTVS DY VKFPGIE TLLPPNAKGQ NITSTLEIRE CIGVEVHRAS GLMAGFLFRG CHFCKMVDAN NPSGGKDGII TFENLSGDWG KGN YVIGGR TSYGSVSSAQ FLRNNGGFER DGGVIGFTSY RAGESGVKTW QGTVGSTTSR NYNLQFRDSV VIYPVWDGFD LGAD TDMNP ELDRPGDYPI TQYPLHQLPL NHLIDNLLVR GALGVGFGMD GKGMYVSNIT VEDCAGSGAY LLTHESVFTN IAIID TNTK DFQANQIYIS GACRVNGLRL IGIRSTDGQG LTIDAPNSTV SGITGMVDPS RINVANLAEE GLGNIRANSF GYDSAA IKL RIHKLSKTLD SGALYSHING GAGSGSAYTQ LTAISGSTPD AVSLKVNHKD CRGAEIPFVP DIASDDFIKD SSCFLPY WE NNSTSLKALV KKPNGELVRL TLATL

UniProtKB: Tail spike protein

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Macromolecule #2: Packaged DNA stabilization protein gp10

MacromoleculeName: Packaged DNA stabilization protein gp10 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 52.51202 KDa
SequenceString: MPIQQLPMMK GMGKDFKNAD YIDYLPVNML ATPKEILNSS GYLRSFPGIT KRYDMNGVSR GVEYNTAQNA VYRVCGGKLY KGESEVGDV AGSGRVSMAH GRTSQAVGVN GQLVEYRYDG TVKTVSNWPA DSGFTQYELG SVRDITRLRG RYAWSKDGTD S WFITDLED ...String:
MPIQQLPMMK GMGKDFKNAD YIDYLPVNML ATPKEILNSS GYLRSFPGIT KRYDMNGVSR GVEYNTAQNA VYRVCGGKLY KGESEVGDV AGSGRVSMAH GRTSQAVGVN GQLVEYRYDG TVKTVSNWPA DSGFTQYELG SVRDITRLRG RYAWSKDGTD S WFITDLED ESHPDRYSAQ YRAESQPDGI IGIGTWRDFI VCFGSSTIEY FSLTGATTAG AALYVAQPSL MVQKGIAGTY CK TPFADSY AFISHPATGA PSVYIIGSGQ ASPIATASIE KIIRSYTAEE MATGVMETLR FDSHELLIIH LPRHVLVYDA SSS QNGPQW CVLKTGLYDD VYRGVDFMYE GNQITCGDKS EAVVGQLQFD ISSQYDKQQE HLLFTPLFKA DNARCFDLEV ESST GVAQY ADRLFLSATT DGINYGREQM IEQNEPFVYD KRVLWKRVGR IRRLIGFKLR VITKSPVTLS GCQIRLE

UniProtKB: Packaged DNA stabilization protein gp10

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.015 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.1 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 29000 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Average electron dose: 1.08 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 41597
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6 / Avg.num./class: 40000
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38155
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8tvr:
In situ cryo-EM structure of bacteriophage P22 tail hub protein: tailspike protein complex at 2.8A resolution

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