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Yorodumi- EMDB-41792: In situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10:... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41792 | |||||||||
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Title | In situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10: gp9 N-term complex in conformation 2 at 3.1A resolution | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phage / 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 portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral procapsid maturation ...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 portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral procapsid maturation / 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 / metabolic process / viral capsid / hydrolase activity / virion attachment to host cell / identical protein binding Similarity search - Function | |||||||||
Biological species | Salmonella phage P22 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Iglesias S / Feng-Hou C / Cingolani G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41792.map.gz | 227.9 MB | EMDB map data format | |
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Header (meta data) | emd-41792-v30.xml emd-41792.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41792_fsc.xml | 15.5 KB | Display | FSC data file |
Images | emd_41792.png | 59.2 KB | ||
Masks | emd_41792_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-41792.cif.gz | 7.4 KB | ||
Others | emd_41792_half_map_1.map.gz emd_41792_half_map_2.map.gz | 259.4 MB 259.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41792 | HTTPS FTP |
-Related structure data
Related structure data | 8u11MC 8tvrC 8tvuC 8u10C 8u1oC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41792.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.16582 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41792_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41792_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41792_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Salmonella phage P22
Entire | Name: Salmonella phage P22 (virus) |
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Components |
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-Supramolecule #1: Salmonella phage P22
Supramolecule | Name: 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 |
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Host (natural) | Organism: Salmonella enterica (bacteria) |
-Macromolecule #1: Packaged DNA stabilization protein gp10
Macromolecule | Name: Packaged DNA stabilization protein gp10 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella phage P22 (virus) |
Molecular weight | Theoretical: 52.51202 KDa |
Sequence | String: 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 |
-Macromolecule #2: Tail spike protein
Macromolecule | Name: Tail spike protein / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella phage P22 (virus) |
Molecular weight | Theoretical: 71.923523 KDa |
Sequence | String: 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 |
-Macromolecule #3: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella phage P22 (virus) |
Molecular weight | Theoretical: 82.829375 KDa |
Sequence | String: 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 |
-Macromolecule #4: Peptidoglycan hydrolase gp4
Macromolecule | Name: Peptidoglycan hydrolase gp4 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella phage P22 (virus) |
Molecular weight | Theoretical: 18.044959 KDa |
Sequence | String: MQIKTKGDLV RAALRKLGVA SDATLTDVEP QSMQDAVDDL EAMMAEWYQD GKGIITGYVF SDDENPPAEG DDHGLRSSAV SAVFHNLAC RIAPDYALEA TAKIIATAKY GKELLYKQTA ISRAKRAPYP SRMPTGSGNS FANLNEWHYF PGEQNADSTT P HDEGNG UniProtKB: Peptidoglycan hydrolase gp4 |
-Macromolecule #5: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 5 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella phage P22 (virus) |
Molecular weight | Theoretical: 46.795613 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film 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 |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8u11: |