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

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Basic information

Entry
Database: PDB / ID: 7sfs
TitleIn situ cryo-EM structure of bacteriophage Sf6 portal:gp7 complex at 2.7A resolution
Components
  • Gene 3 protein
  • Gene 7 protein
KeywordsSTRUCTURAL PROTEIN / in situ / phage / portal / gp7 / gp3
Function / homologyTail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / symbiont genome ejection through host cell envelope, short tail mechanism / metal ion binding / Gene 7 protein / Gene 3 protein
Function and homology information
Biological speciesShigella phage Sf6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 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
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Gene 3 protein
A: Gene 3 protein
B: Gene 3 protein
C: Gene 3 protein
D: Gene 3 protein
E: Gene 3 protein
F: Gene 3 protein
G: Gene 3 protein
H: Gene 3 protein
I: Gene 3 protein
J: Gene 3 protein
K: Gene 3 protein
N: Gene 7 protein
O: Gene 7 protein
P: Gene 7 protein
Q: Gene 7 protein
R: Gene 7 protein
S: Gene 7 protein
T: Gene 7 protein
U: Gene 7 protein
V: Gene 7 protein
W: Gene 7 protein
X: Gene 7 protein
L: Gene 7 protein


Theoretical massNumber of molelcules
Total (without water)1,167,74524
Polymers1,167,74524
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area226560 Å2
ΔGint-762 kcal/mol
Surface area377960 Å2

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Components

#1: Protein
Gene 3 protein


Mass: 79558.227 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716H2
#2: Protein
Gene 7 protein


Mass: 17753.889 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716G8

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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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
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

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
2RELION3.1.2image acquisition
4RELION3.1.2CTF correction
13RELION3.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 67439
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 108.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006774613
ELECTRON MICROSCOPYf_angle_d0.7569100943
ELECTRON MICROSCOPYf_chiral_restr0.048910914
ELECTRON MICROSCOPYf_plane_restr0.006213412
ELECTRON MICROSCOPYf_dihedral_angle_d5.330910244

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