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- PDB-7ukj: In situ cryo-EM structure of bacteriophage Sf6 portal:gp7 complex... -

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Basic information

Entry
Database: PDB / ID: 7ukj
TitleIn situ cryo-EM structure of bacteriophage Sf6 portal:gp7 complex at 2.7A resolution
ComponentsGene 14 protein
KeywordsVIRAL PROTEIN / in situ / phage / portal / gp7 / gp3 / structural protein
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component
Similarity search - Function
: / Tailspike protein, C-terminal / 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
Biological speciesShigella phage Sf6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi, F. / Cingolani, G. / Hou, C.
Funding support United States, 1items
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
DepositionApr 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.0Dec 21, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 21, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 21, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 21, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 21, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 21, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 21, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gene 14 protein
B: Gene 14 protein
C: Gene 14 protein


Theoretical massNumber of molelcules
Total (without water)201,3543
Polymers201,3543
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Gene 14 protein


Mass: 67118.141 Da / Num. of mol.: 3 / Fragment: Tailspike / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716G1
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Shigella virus Sf6 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella virus Sf6
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7977

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2RELION3.1.2image acquisition
4RELION3.1.2CTF correction
8PHENIXmodel refinement
13RELION3.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 67439
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314477
ELECTRON MICROSCOPYf_angle_d0.58519714
ELECTRON MICROSCOPYf_dihedral_angle_d4.8872014
ELECTRON MICROSCOPYf_chiral_restr0.0482256
ELECTRON MICROSCOPYf_plane_restr0.0052592

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