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- PDB-8ean: Cryo-EM structure of in-situ tailspike in bacteriophage P22 -

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Basic information

Entry
Database: PDB / ID: 8ean
TitleCryo-EM structure of in-situ tailspike in bacteriophage P22
ComponentsTail spike protein
KeywordsVIRAL PROTEIN / Bacteriophage P22
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell
Similarity search - Function
Tailspike Protein; Chain / Phage P22 tailspike-like, N-terminal domain / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, C. / Liu, J. / Molineux, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: In-situ structure of tail machine reveals mechanistic insights into P22 assembly.
Authors: Wang, C. / Liu, J. / Molineux, I.J.
History
DepositionAug 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Tail spike protein
Y: Tail spike protein
Z: Tail spike protein


Theoretical massNumber of molelcules
Total (without water)214,0863
Polymers214,0863
Non-polymers00
Water00
1


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

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Components

#1: Protein Tail spike protein / TSP / Endo-1 / 3-alpha-L-rhamnosidase / Endorhamnosidase / Gene product 9 / gp9


Mass: 71361.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus)
References: UniProt: P12528, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
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: Cryo-EM structure of in-situ tailspike from bacteriophage P22
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella phage P22 (virus)
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195900 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415394
ELECTRON MICROSCOPYf_angle_d0.58220918
ELECTRON MICROSCOPYf_dihedral_angle_d5.3632138
ELECTRON MICROSCOPYf_chiral_restr0.0462348
ELECTRON MICROSCOPYf_plane_restr0.0032744

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