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- EMDB-41791: In situ cryo-EM structure of bacteriophage P22 gp1:gp4:gp5:gp10:g... -

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Entry
Database: EMDB / ID: EMD-41791
TitleIn situ cryo-EM structure of bacteriophage P22 gp1:gp4:gp5:gp10:gp9 N-term complex in conformation 1 at 3.2A resolution
Map data
Sample
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Packaged DNA stabilization protein gp10
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Peptidoglycan hydrolase gp4
Keywordsphage / bacteriophage / tail spike protein / TSP / gene product 9 (gp9) / Packaged DNA stabilization protein / gene product 10 (gp10) / STRUCTURAL PROTEIN / VIRAL PROTEIN / head-to-tail protein / gene product 4 (gp4) / Tail hub protein / gene product (1) / Portal protein / Coat protein / Major capsid protein / gene product 5 (gp5)
Function / homology
Function and homology information


viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral procapsid / viral portal complex / virus tail, fiber / viral procapsid maturation / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope ...viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral procapsid / viral portal complex / virus tail, fiber / viral procapsid maturation / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / virus tail / symbiont entry into host / T=7 icosahedral viral capsid / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion assembly / viral capsid / hydrolase activity / virion attachment to host cell / identical protein binding
Similarity search - Function
Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / Major capsid protein Gp5 / P22 coat protein - gene protein 5 / P22 tailspike C-terminal domain ...Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / Major capsid protein Gp5 / P22 coat protein - gene protein 5 / 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 / Portal protein / Head-to-tail adapter protein gp4 / Major capsid protein / Tail hub protein gp10
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsIglesias S / Feng-Hou C / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)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 30, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41791.png

Downloads & links

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Map

FileDownload / File: emd_41791.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.17 Å/pix.
x 440 pix.
= 512.96 Å		1.17 Å/pix.
x 440 pix.
= 512.96 Å		1.17 Å/pix.
x 440 pix.
= 512.96 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16582 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-14.9358635 - 20.218468000000001
Average (Standard dev.)-0.000000000003213 (±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_41791_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_41791_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_41791_half_map_2.map
Projections & Slices
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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: Portal protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Packaged DNA stabilization protein gp10
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Peptidoglycan hydrolase gp4

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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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 82.829375 KDa
SequenceString: MADNENRLES ILSRFDADWT ASDEARREAK NDLFFSRVSQ WDDWLSQYTT LQYRGQFDVV RPVVRKLVSE MRQNPIDVLY RPKDGARPD AADVLMGMYR TDMRHNTAKI AVNIAVREQI EAGVGAWRLV TDYEDQSPTS NNQVIRREPI HSACSHVIWD S NSKLMDKS ...String:
MADNENRLES ILSRFDADWT ASDEARREAK NDLFFSRVSQ WDDWLSQYTT LQYRGQFDVV RPVVRKLVSE MRQNPIDVLY RPKDGARPD AADVLMGMYR TDMRHNTAKI AVNIAVREQI EAGVGAWRLV TDYEDQSPTS NNQVIRREPI HSACSHVIWD S NSKLMDKS DARHCTVIHS MSQNGWEDFA EKYDLDADDI PSFQNPNDWV FPWLTQDTIQ IAEFYEVVEK KETAFIYQDP VT GEPVSYF KRDIKDVIDD LADSGFIKIA ERQIKRRRVY KSIITCTAVL KDKQLIAGEH IPIVPVFGEW GFVEDKEVYE GVV RLTKDG QRLRNMIMSF NADIVARTPK KKPFFWPEQI AGFEHMYDGN DDYPYYLLNR TDENSGDLPT QPLAYYENPE VPQA NAYML EAATSAVKEV ATLGVDTEAV NGGQVAFDTV NQLNMRADLE TYVFQDNLAT AMRRDGEIYQ SIVNDIYDVP RNVTI TLED GSEKDVQLMA EVVDLATGEK QVLNDIRGRY ECYTDVGPSF QSMKQQNRAE ILELLGKTPQ GTPEYQLLLL QYFTLL DGK GVEMMRDYAN KQLIQMGVKK PETPEEQQWL VEAQQAKQGQ QDPAMVQAQG VLLQGQAELA KAQNQTLSLQ IDAAKVE AQ NQLNAARIAE IFNNMDLSKQ SEFREFLKTV ASFQQDRSED ARANAELLLK GDEQTHKQRM DIANILQSQR QNQPSGSV A ETPQ

UniProtKB: Portal protein

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 46.795613 KDa
SequenceString: MALNEGQIVT LAVDEIIETI SAITPMAQKA KKYTPPAASM QRSSNTIWMP VEQESPTQEG WDLTDKATGL LELNVAVNMG EPDNDFFQL RADDLRDETA YRRRIQSAAR KLANNVELKV ANMAAEMGSL VITSPDAIGT NTADAWNFVA DAEEIMFSRE L NRDMGTSY ...String:
MALNEGQIVT LAVDEIIETI SAITPMAQKA KKYTPPAASM QRSSNTIWMP VEQESPTQEG WDLTDKATGL LELNVAVNMG EPDNDFFQL RADDLRDETA YRRRIQSAAR KLANNVELKV ANMAAEMGSL VITSPDAIGT NTADAWNFVA DAEEIMFSRE L NRDMGTSY FFNPQDYKKA GYDLTKRDIF GRIPEEAYRD GTIQRQVAGF DDVLRSPKLP VLTKSTATGI TVSGAQSFKP VA WQLDNDG NKVNVDNRFA TVTLSATTGM KRGDKISFAG VKFLGQMAKN VLAQDATFSV VRVVDGTHVE ITPKPVALDD VSL SPEQRA YANVNTSLAD AMAVNILNVK DARTNVFWAD DAIRIVSQPI PANHELFAGM KTTSFSIPDV GLNGIFATQG DIST LSGLC RIALWYGVNA TRPEAIGVGL PGQTA

UniProtKB: Major capsid protein

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Macromolecule #3: Packaged DNA stabilization protein gp10

MacromoleculeName: Packaged DNA stabilization protein gp10 / type: protein_or_peptide / ID: 3 / 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: Tail hub protein gp10

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Macromolecule #4: Tail spike protein

MacromoleculeName: Tail spike protein / type: protein_or_peptide / ID: 4 / 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 #5: Peptidoglycan hydrolase gp4

MacromoleculeName: Peptidoglycan hydrolase gp4 / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 18.044959 KDa
SequenceString:
MQIKTKGDLV RAALRKLGVA SDATLTDVEP QSMQDAVDDL EAMMAEWYQD GKGIITGYVF SDDENPPAEG DDHGLRSSAV SAVFHNLAC RIAPDYALEA TAKIIATAKY GKELLYKQTA ISRAKRAPYP SRMPTGSGNS FANLNEWHYF PGEQNADSTT P HDEGNG

UniProtKB: Head-to-tail adapter protein gp4

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 18053
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8u10:
In situ cryo-EM structure of bacteriophage P22 gp1:gp4:gp5:gp10:gp9 N-term complex in conformation 1 at 3.2A resolution

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