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- PDB-8eb7: Cryo-EM structure of the in-situ gp4-gp10-gp9N from bacteriophage P22 -

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Basic information

Entry
Database: PDB / ID: 8eb7
TitleCryo-EM structure of the in-situ gp4-gp10-gp9N from bacteriophage P22
Components
  • Packaged DNA stabilization protein gp10
  • Peptidoglycan hydrolase gp4
  • Tail 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 / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / virus tail / 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 ...endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / virus tail / 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 / metabolic process / hydrolase activity / virion attachment to host cell
Similarity search - Function
Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / 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 ...Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / 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
Similarity search - Domain/homology
Tail spike protein / Peptidoglycan hydrolase gp4 / Packaged DNA stabilization protein gp10
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Tail spike protein
A: Tail spike protein
B: Tail spike protein
C: Tail spike protein
D: Tail spike protein
E: Peptidoglycan hydrolase gp4
F: Tail spike protein
G: Peptidoglycan hydrolase gp4
H: Peptidoglycan hydrolase gp4
I: Peptidoglycan hydrolase gp4
J: Peptidoglycan hydrolase gp4
K: Peptidoglycan hydrolase gp4
L: Peptidoglycan hydrolase gp4
M: Peptidoglycan hydrolase gp4
N: Peptidoglycan hydrolase gp4
O: Peptidoglycan hydrolase gp4
P: Peptidoglycan hydrolase gp4
Q: Peptidoglycan hydrolase gp4
R: Packaged DNA stabilization protein gp10
S: Packaged DNA stabilization protein gp10
T: Packaged DNA stabilization protein gp10
U: Packaged DNA stabilization protein gp10
V: Packaged DNA stabilization protein gp10
W: Packaged DNA stabilization protein gp10
X: Tail spike protein
Y: Tail spike protein
Z: Tail spike protein
a: Tail spike protein
b: Tail spike protein
c: Tail spike protein
d: Tail spike protein
e: Tail spike protein
f: Tail spike protein
g: Tail spike protein
h: Tail spike protein
i: Tail spike protein


Theoretical massNumber of molelcules
Total (without water)729,05536
Polymers729,05536
Non-polymers00
Water0
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: 12126.580 Da / Num. of mol.: 18 / 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
#2: Protein
Peptidoglycan hydrolase gp4 / Gene product 4 / Gp4 / Internal virion protein gp4 / Tail adapter protein gp4


Mass: 16359.296 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26746
#3: Protein
Packaged DNA stabilization protein gp10


Mass: 52410.852 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26749

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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 the in-situ gp4-gp10-gp9N 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 FIELDBright-field microscopy / 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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32650 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00452332
ELECTRON MICROSCOPYf_angle_d0.62971100
ELECTRON MICROSCOPYf_dihedral_angle_d4.6517248
ELECTRON MICROSCOPYf_chiral_restr0.0497854
ELECTRON MICROSCOPYf_plane_restr0.0059330

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