[English] 日本語
Yorodumi- EMDB-41651: In situ cryo-EM structure of bacteriophage P22 portal protein: he... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41651 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | In situ cryo-EM structure of bacteriophage P22 portal protein: head-to-tail protein complex at 3.0A resolution | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | phage / bacteriophage / portal protein / head-to-tail protein / gene product 1 (gp1) / gene product 4 (gp4 / STRUCTURAL PROTEIN / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / 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 / virion assembly / hydrolase activity Similarity search - Function | |||||||||
Biological species | Salmonella phage P22 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Iglesias SM / Cingolani G / Feng-Hou C | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41651.map.gz | 191.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-41651-v30.xml emd-41651.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41651_fsc.xml | 15.5 KB | Display | FSC data file |
Images | emd_41651.png | 41.5 KB | ||
Masks | emd_41651_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-41651.cif.gz | 6.2 KB | ||
Others | emd_41651_half_map_1.map.gz emd_41651_half_map_2.map.gz | 26.1 MB 26.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41651 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41651 | HTTPS FTP |
-Related structure data
Related structure data | 8tvuMC 8tvrC 8u10C 8u11C 8u1oC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_41651.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.16582 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_41651_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_41651_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_41651_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Salmonella phage P22
Entire | Name: Salmonella phage P22 (virus) |
---|---|
Components |
|
-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 |
---|---|
Host (natural) | Organism: Salmonella enterica (bacteria) |
-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
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 #2: Peptidoglycan hydrolase gp4
Macromolecule | Name: Peptidoglycan hydrolase gp4 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
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 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |