+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14509 | |||||||||
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Title | gp6/gp15/gp16 connector complex of bacteriophage SPP1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bacteriophage / SPP1 / Portal Protein / Head completion proteins / Connector Complex / DNA Channel / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral DNA genome packaging, headful / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / viral procapsid / virion component Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Orlov I / Roche S / Tavares P / Orlova EV | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper. Authors: Igor Orlov / Stéphane Roche / Sandrine Brasilès / Natalya Lukoyanova / Marie-Christine Vaney / Paulo Tavares / Elena V Orlova / Abstract: Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 ...Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 (gp6gp15gp16) in the post-DNA packaging state at 2.7 Å resolution obtained by single particle cryo-electron microscopy. Comparison of the native SPP1 complex with assembly-naïve structures of individual components uncovered the complex program of conformational changes leading to its assembly. After DNA packaging, gp15 binds via its C-terminus to the gp6 oligomer positioning gp15 subunits for oligomerization. Gp15 refolds its inner loops creating an intersubunit β-barrel that establishes different types of contacts with six gp16 subunits. Gp16 binding and oligomerization is accompanied by folding of helices that close the portal channel to keep the viral genome inside the capsid. This mechanism of assembly has broad functional and evolutionary implications for viruses of the prokaryotic tailed viruses-herpesviruses lineage. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14509.map.gz | 351 MB | EMDB map data format | |
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Header (meta data) | emd-14509-v30.xml emd-14509.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_14509.png | 170 KB | ||
Filedesc metadata | emd-14509.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14509 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14509 | HTTPS FTP |
-Validation report
Summary document | emd_14509_validation.pdf.gz | 459 KB | Display | EMDB validaton report |
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Full document | emd_14509_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | emd_14509_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_14509_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14509 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14509 | HTTPS FTP |
-Related structure data
Related structure data | 7z4wMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14509.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.69 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacte...
Entire | Name: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacteriophage |
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Components |
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-Supramolecule #1: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacte...
Supramolecule | Name: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacteriophage type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Strain: YB886 |
Molecular weight | Theoretical: 0.902 kDa/nm |
-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 57.390277 KDa |
Sequence | String: MADIYPLGKT HTEELNEIIV ESAKEIAEPD TTMIQKLIDE HNPEPLLKGV RYYMCENDIE KKRRTYYDAA GQQLVDDTKT NNRTSHAWH KLFVDQKTQY LVGEPVTFTS DNKTLLEYVN ELADDDFDDI LNETVKNMSN KGIEYWHPFV DEEGEFDYVI F PAEEMIVV ...String: MADIYPLGKT HTEELNEIIV ESAKEIAEPD TTMIQKLIDE HNPEPLLKGV RYYMCENDIE KKRRTYYDAA GQQLVDDTKT NNRTSHAWH KLFVDQKTQY LVGEPVTFTS DNKTLLEYVN ELADDDFDDI LNETVKNMSN KGIEYWHPFV DEEGEFDYVI F PAEEMIVV YKDNTRRDIL FALRYYSYKG IMGEETQKAE LYTDTHVYYY EKIDGVYQMD YSYGENNPRP HMTKGGQAIG WG RVPIIPF KNNEEMVSDL KFYKDLIDNY DSITSSTMDS FSDFQQIVYV LKNYDGENPK EFTANLRYHS VIKVSGDGGV DTL RAEIPV DSAAKELERI QDELYKSAQA VDNSPETIGG GATGPALENL YALLDLKANM AERKIRAGLR LFFWFFAEYL RNTG KGDFN PDKELTMTFT RTRIQNDSEI VQSLVQGVTG GIMSKETAVA RNPFVQDPEE ELARIEEEMN QYAEMQGNLL DDEGG DDDL EEDDPNAGAA ESGGAGQVS UniProtKB: Portal protein |
-Macromolecule #2: Head completion protein gp15
Macromolecule | Name: Head completion protein gp15 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 11.629402 KDa |
Sequence | String: MDIQRVKRLL SITNDKHDEY LTEMVPLLVE FAKDECHNPF IDKDGNESIP SGVLIFVAKA AQFYMTNAGL TGRSMDTVSY NFATEIPST ILKKLNPYRK MAR UniProtKB: Head completion protein gp15 |
-Macromolecule #3: Head completion protein gp16
Macromolecule | Name: Head completion protein gp16 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 12.55499 KDa |
Sequence | String: MYEEFPDVIT FQSYVEQSNG EGGKTYKWVD EFTAAAHVQP ISQEEYYKAQ QLQTPIGYNI YTPYDDRIDK KMRVIYRGKI VTFIGDPVD LSGLQEITRI KGKEDGAYVG UniProtKB: Head completion protein gp16 |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 406 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.64 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3876 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 120000 |
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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Residue range: 254-344 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Manual inspection of the residues in the complete gp6, gp15 and gp16 polypeptide chains tracing was done using COOT and refined in Phenix |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 90 |
Output model | PDB-7z4w: |