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Yorodumi- EMDB-25106: In situ cryo-EM structure of bacteriophage Sf6 gp8:gp14N complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25106 | |||||||||
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Title | In situ cryo-EM structure of bacteriophage Sf6 gp8:gp14N complex at 2.8 A resolution | |||||||||
Map data | ||||||||||
Sample |
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Keywords | in situ / phage / gp8 / gp14 / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information virus tail / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | Shigella phage Sf6 (virus) / Shigella virus Sf6 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Li F / Cingolani G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2022 Title: High-resolution cryo-EM structure of the virus Sf6 genome delivery tail machine. Authors: Fenglin Li / Chun-Feng David Hou / Ruoyu Yang / Richard Whitehead / Carolyn M Teschke / Gino Cingolani / Abstract: Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom ...Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25106.map.gz | 396.7 MB | EMDB map data format | |
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Header (meta data) | emd-25106-v30.xml emd-25106.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25106_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_25106.png | 109.5 KB | ||
Filedesc metadata | emd-25106.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25106 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25106 | HTTPS FTP |
-Validation report
Summary document | emd_25106_validation.pdf.gz | 628.7 KB | Display | EMDB validaton report |
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Full document | emd_25106_full_validation.pdf.gz | 628.3 KB | Display | |
Data in XML | emd_25106_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_25106_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25106 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25106 | HTTPS FTP |
-Related structure data
Related structure data | 7sg7MC 7sfsC 7sp4C 7spuC 7ukjC 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_25106.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.122 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Shigella virus Sf6
Entire | Name: Shigella virus Sf6 |
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Components |
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-Supramolecule #1: Shigella virus Sf6
Supramolecule | Name: Shigella virus Sf6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10761 / Sci species name: Shigella virus Sf6 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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-Macromolecule #1: Gene 14 protein
Macromolecule | Name: Gene 14 protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella phage Sf6 (virus) |
Molecular weight | Theoretical: 67.118141 KDa |
Sequence | String: MTDIITNVVI GMPSQLFTMA RSFKAVANGK IYIGKIDTDP VNPENQIQVY VENEDGSHVP VSQPIVINAA GYPVYNGQIA KFVTEQGHS MAVYDAYGSQ QFYFQNVLKY DPDQFGPDLI EQLAQSGKYS QDNTKGDAMI GVKQPLPKAV LRTQHDKNKE A ISILDFGV ...String: MTDIITNVVI GMPSQLFTMA RSFKAVANGK IYIGKIDTDP VNPENQIQVY VENEDGSHVP VSQPIVINAA GYPVYNGQIA KFVTEQGHS MAVYDAYGSQ QFYFQNVLKY DPDQFGPDLI EQLAQSGKYS QDNTKGDAMI GVKQPLPKAV LRTQHDKNKE A ISILDFGV IDDGVTDNYQ AIQNAIDAVA SLPSGGELFI PASNQAVGYI VGSTLLIPGG VNIRGVGKAS QLRAKSGLTG SV LRLSYDS DTIGRYLRNI RVTGNNTCNG IDTNITAEDS VIRQVYGWVF DNVMVNEVET AYLMQGLWHS KFIACQAGTC RVG LHFLGQ CVSVSVSSCH FSRGNYSADE SFGIRIQPQT YAWSSEAVRS EAIILDSETM CIGFKNAVYV HDCLDLHMEQ LDLD YCGST GVVIENVNGG FSFSNSWIAA DADGTEQFTG IYFRTPTSTQ SHKIVSGVHI NTANKNTAAN NQSIAIEQSA IFVFV SGCT LTGDEWAVNI VDINECVSFD KCIFNKPLRY LRSGGVSVTD CYLAGITEVQ KPEGRYNTYR GCSGVPSVNG IINVPV AVG ATSGSAAIPN PGNLTYRVRS LFGDPASSGD KVSVSGVTIN VTRPSPVGVA LPSMVEYLAI UniProtKB: Gene 14 protein |
-Macromolecule #2: Gene 8 protein
Macromolecule | Name: Gene 8 protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella phage Sf6 (virus) |
Molecular weight | Theoretical: 52.204586 KDa |
Sequence | String: MPIQQLPLMK GVGKDFRNAD YIDYLPVNML ATPKEILNSS GYLRSFPGIA KRSDVNGVSR GVEYNMAQNA VYRVCGGKLY KGESEVGDV AGSGRVSMAH GRTSQAVGVN GQLVEYRYDG TVKTVSNWPT DSGFTQYELG SVRDITRLRG RYAWSKDGTD S WFITDLED ...String: MPIQQLPLMK GVGKDFRNAD YIDYLPVNML ATPKEILNSS GYLRSFPGIA KRSDVNGVSR GVEYNMAQNA VYRVCGGKLY KGESEVGDV AGSGRVSMAH GRTSQAVGVN GQLVEYRYDG TVKTVSNWPT DSGFTQYELG SVRDITRLRG RYAWSKDGTD S WFITDLED ESHPDRYSAQ YRAESQPDGI IGIGTWRDFI VCFGSSTIEY FSLTGATTAG AALYVAQPSL MVQKGIAGTY CK TPFADSY AFISNPATGA PSVYIIGSGQ VSPIASASIE KILRSYTADE LADGVMESLR FDAHELLIIH LPRHVLVYDA SSS ANGPQW CVLKTGLYDD VYRAIDFIYE GNQITCGDKL ESVTGKLQFD ISSQYGLQQE HLLFTPLFKA DNARCFDLEV ESST GVAQY ADRLFLSATT DGINYGREQM IEQNEPFVYD KRVLWKRVGR IRKNVGFKLR VITKSPVTLS GAQIRIE UniProtKB: Gene 8 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 |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 7977 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |