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- PDB-6zig: Topological model of the p2 virion baseplate in activated conform... -

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Basic information

Entry
Database: PDB / ID: 6zig
TitleTopological model of the p2 virion baseplate in activated conformation (closed Tal trimer)
Components
  • Baseplate protein gp16
  • Distal tail protein
  • Receptor binding protein
KeywordsVIRAL PROTEIN / lactococcal siphophage p2 / baseplate / receptor-binding protein / Distal Tail protein / Tail-associated lysin
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Phage tail base-plate attachment protein ORF16 / Baseplate protein Gp15-like / Baseplate protein Gp16, domain D4 / Baseplate protein Gp16, domain 1 and 2 / : / : / : / : / Distal tail protein, N-terminal domain / Phage tail base-plate attachment protein N-terminal barrel domain ...Phage tail base-plate attachment protein ORF16 / Baseplate protein Gp15-like / Baseplate protein Gp16, domain D4 / Baseplate protein Gp16, domain 1 and 2 / : / : / : / : / Distal tail protein, N-terminal domain / Phage tail base-plate attachment protein N-terminal barrel domain / Phage tail base-plate attachment protein C-terminal insertion domain / Phage tail base-plate attachment protein N0 domain / Phage tail base-plate attachment protein C-terminal barrel domain / Dit, C-terminal domain / : / Lactococcus phage p2, Receptor binding protein, neck domain / : / Lactophage receptor-binding protein N-terminal shoulder domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Baseplate protein gp16 / Distal tail protein / Receptor binding protein
Similarity search - Component
Biological speciesLactococcus phage p2 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 42.2 Å
AuthorsSpinelli, S. / Cambillau, C. / Goulet, A.
CitationJournal: Viruses / Year: 2020
Title: Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism.
Authors: Silvia Spinelli / Denise Tremblay / Sylvain Moineau / Christian Cambillau / Adeline Goulet /
Abstract: Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated ...Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected.
History
DepositionJun 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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  • EMDB-11225
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Receptor binding protein
B: Receptor binding protein
C: Receptor binding protein
D: Receptor binding protein
E: Receptor binding protein
F: Receptor binding protein
G: Receptor binding protein
H: Receptor binding protein
I: Receptor binding protein
J: Receptor binding protein
K: Receptor binding protein
L: Receptor binding protein
M: Receptor binding protein
N: Receptor binding protein
O: Receptor binding protein
P: Receptor binding protein
Q: Receptor binding protein
R: Receptor binding protein
S: Distal tail protein
T: Distal tail protein
U: Distal tail protein
V: Distal tail protein
W: Distal tail protein
X: Distal tail protein
Y: Baseplate protein gp16
Z: Baseplate protein gp16
1: Baseplate protein gp16
2: Distal tail protein
3: Distal tail protein
4: Distal tail protein
5: Distal tail protein
6: Distal tail protein
7: Distal tail protein


Theoretical massNumber of molelcules
Total (without water)1,058,81933
Polymers1,058,81933
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Receptor binding protein / RBP / Gene product 18 / Gp18 / Coordinate model: Cα atoms only


Mass: 28668.057 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage p2 (virus) / References: UniProt: Q71AW2
#2: Protein
Distal tail protein / Dit / Gene product 15 / Gp15 / Coordinate model: Cα atoms only


Mass: 34511.992 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage p2 (virus) / References: UniProt: D3WAD3
#3: Protein Baseplate protein gp16 / Gene product 16 / Gp16 / Tail-associated lysine-like protein / Coordinate model: Cα atoms only


Mass: 42883.266 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage p2 (virus) / References: UniProt: D3KFX4

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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: Lactococcus virus P2 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Lactococcus virus P2
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Lactococcus lactis
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl acetate

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Film or detector model: OTHER

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 293
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 42.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12X53

2x53

12X531PDBexperimental model
22WZP

2wzp

12WZP2PDBexperimental model

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