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- EMDB-25106: In situ cryo-EM structure of bacteriophage Sf6 gp8:gp14N complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-25106
TitleIn situ cryo-EM structure of bacteriophage Sf6 gp8:gp14N complex at 2.8 A resolution
Map data
Sample
  • Virus: Shigella virus Sf6
    • Protein or peptide: Gene 14 protein
    • Protein or peptide: Gene 8 protein
Keywordsin 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
: / Tailspike protein, C-terminal / Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Gene 14 protein / Gene 8 protein
Similarity search - Component
Biological speciesShigella phage Sf6 (virus) / Shigella virus Sf6
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLi F / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: 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
DepositionOct 5, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25106.png

Downloads & links

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Map

FileDownload / File: emd_25106.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.122 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.02305713 - 0.06289392
Average (Standard dev.)-0.000030357754 (±0.004561279)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 574.464 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Shigella virus Sf6

EntireName: Shigella virus Sf6
Components
  • Virus: Shigella virus Sf6
    • Protein or peptide: Gene 14 protein
    • Protein or peptide: Gene 8 protein

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Supramolecule #1: Shigella virus Sf6

SupramoleculeName: 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

MacromoleculeName: Gene 14 protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf6 (virus)
Molecular weightTheoretical: 67.118141 KDa
SequenceString: 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

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Macromolecule #2: Gene 8 protein

MacromoleculeName: Gene 8 protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf6 (virus)
Molecular weightTheoretical: 52.204586 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7977 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 67439
Startup modelType of model: PDB ENTRY
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 39000
FSC plot (resolution estimation)

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