[English] 日本語
Yorodumi- EMDB-4051: bacteriophage phi812K1-420 tail sheath and tail tube protein in n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4051 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | bacteriophage phi812K1-420 tail sheath and tail tube protein in native tail | |||||||||||||||||||||
Map data | bacteriophage ph812K1-420 native tail | |||||||||||||||||||||
Sample |
| |||||||||||||||||||||
Keywords | polyvalent staphylococcal bactoriophage / Myoviridae / tail sheath / tail contraction / viral protein | |||||||||||||||||||||
Function / homology | Phage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Major tail sheath protein / Phage-like element PBSX protein XkdM Function and homology information | |||||||||||||||||||||
Biological species | Staphylococcus phage 812 (virus) / Staphylococcus (bacteria) | |||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||||||||||||||
Authors | Novacek J / Siborova M / Benesik M / Pantucek R / Doskar J / Plevka P | |||||||||||||||||||||
Funding support | Czech Republic, 6 items
| |||||||||||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2016 Title: Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate. Authors: Jiří Nováček / Marta Šiborová / Martin Benešík / Roman Pantůček / Jiří Doškař / Pavel Plevka / Abstract: Bacteriophages from the family Myoviridae use double-layered contractile tails to infect bacteria. Contraction of the tail sheath enables the tail tube to penetrate through the bacterial cell wall ...Bacteriophages from the family Myoviridae use double-layered contractile tails to infect bacteria. Contraction of the tail sheath enables the tail tube to penetrate through the bacterial cell wall and serve as a channel for the transport of the phage genome into the cytoplasm. However, the mechanisms controlling the tail contraction and genome release of phages with "double-layered" baseplates were unknown. We used cryo-electron microscopy to show that the binding of the Twort-like phage phi812 to the Staphylococcus aureus cell wall requires a 210° rotation of the heterohexameric receptor-binding and tripod protein complexes within its baseplate about an axis perpendicular to the sixfold axis of the tail. This rotation reorients the receptor-binding proteins to point away from the phage head, and also results in disruption of the interaction of the tripod proteins with the tail sheath, hence triggering its contraction. However, the tail sheath contraction of Myoviridae phages is not sufficient to induce genome ejection. We show that the end of the phi812 double-stranded DNA genome is bound to one protein subunit from a connector complex that also forms an interface between the phage head and tail. The tail sheath contraction induces conformational changes of the neck and connector that result in disruption of the DNA binding. The genome penetrates into the neck, but is stopped at a bottleneck before the tail tube. A subsequent structural change of the tail tube induced by its interaction with the S. aureus cell is required for the genome's release. | |||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4051.map.gz | 9.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4051-v30.xml emd-4051.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_4051.png | 309.6 KB | ||
Filedesc metadata | emd-4051.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4051 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4051 | HTTPS FTP |
-Validation report
Summary document | emd_4051_validation.pdf.gz | 267.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4051_full_validation.pdf.gz | 266.6 KB | Display | |
Data in XML | emd_4051_validation.xml.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4051 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4051 | HTTPS FTP |
-Related structure data
Related structure data | 5li2MC 4003C 4052C 4053C 4054C 8201C 8202C 8203C 8204C 8205C 8206C 8207C 8208C 8209C 8210C 8211C 8212C 8213C 8214C 8304C 5li4C 5liiC 5lijC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_4051.map.gz / Format: CCP4 / Size: 32.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | bacteriophage ph812K1-420 native tail | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Staphylococcus phage 812
Entire | Name: Staphylococcus phage 812 (virus) |
---|---|
Components |
|
-Supramolecule #1: Staphylococcus phage 812
Supramolecule | Name: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Sci species strain: K420 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: Staphylococcus aureus (bacteria) |
Virus shell | Shell ID: 1 / Diameter: 1100.0 Å / T number (triangulation number): 16 |
-Macromolecule #1: tail sheath protein
Macromolecule | Name: tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Staphylococcus phage 812 (virus) |
Molecular weight | Theoretical: 64.559008 KDa |
Recombinant expression | Organism: Staphylococcaceae (Staphylococcus group) |
Sequence | String: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS ...String: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS VEHDEETQKA SRLVLKVGDQ EVKSYDLTGG AYDYTNAIIT DINQLPDFEA KLSPFGDKNL ESSKLDKIEN AN IKDKAVY VKAVFGDLEK QTAYNGIVSF EQLNAEGEVP SNVEVEAGEE SATVTATSPI KTIEPFELTK LKGGTNGEPP ATW ADKLDK FAHEGGYYIV PLSSKQSVHA EVASFVKERS DAGEPMRAIV GGGFNESKEQ LFGRQASLSN PRVSLVANSG TFVM DDGRK NHVPAYMVAV ALGGLASGLE IGESITFKPL RVSSLDQIYE SIDLDELNEN GIISIEFVRN RTNTFFRIVD DVTTF NDKS DPVKAEMAVG EANDFLVSEL KVQLEDQFIG TRTINTSASI IKDFIQSYLG RKKRDNEIQD FPAEDVQVIV EGNEAR ISM TVYPIRSFKK ISVSLVYKQQ TLQA UniProtKB: Major tail sheath protein |
-Macromolecule #2: Phage-like element PBSX protein XkdM
Macromolecule | Name: Phage-like element PBSX protein XkdM / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Staphylococcus (bacteria) |
Molecular weight | Theoretical: 17.445471 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MALKAQNTIS GKEGRLFLDG EEMAHIKTFE ANVEKNKSEV NIMGRRMTGH KTTGANGTGT ATFYKVTSKF VLLMMDYVKK GSDPYFTLQ AVLDDQSSGR GTERVTLYDV NFDSAKIASL DVDSEALEEE VPFTFEDFDV PEKLSDTFLE HHHHHH UniProtKB: Phage-like element PBSX protein XkdM |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 0.86 sec. / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 38.9 Å Applied symmetry - Helical parameters - Δ&Phi: 21.4 ° Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic) Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 3628 |
---|---|
Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE / Software: (Name: SPIDER, IHRSR) |