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- PDB-8eao: Cryo-EM structure of the in-situ gp1-gp4 complex from bacteriopha... -

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Basic information

Entry
Database: PDB / ID: 8eao
TitleCryo-EM structure of the in-situ gp1-gp4 complex from bacteriophage P22
Components
  • Peptidoglycan hydrolase gp4
  • Portal protein
KeywordsVIRAL PROTEIN / Bacteriophage P22
Function / homology
Function and homology information


viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / virus tail / virion assembly / hydrolase activity
Similarity search - Function
Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein
Similarity search - Domain/homology
Portal protein / Peptidoglycan hydrolase gp4
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 1.1Jun 4, 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
A: Peptidoglycan hydrolase gp4
B: Portal protein
C: Peptidoglycan hydrolase gp4
D: Portal protein
E: Peptidoglycan hydrolase gp4
F: Portal protein
G: Peptidoglycan hydrolase gp4
H: Portal protein
I: Peptidoglycan hydrolase gp4
J: Portal protein
K: Peptidoglycan hydrolase gp4
L: Portal protein
M: Peptidoglycan hydrolase gp4
N: Portal protein
O: Peptidoglycan hydrolase gp4
P: Portal protein
Q: Peptidoglycan hydrolase gp4
R: Portal protein
S: Peptidoglycan hydrolase gp4
T: Portal protein
U: Peptidoglycan hydrolase gp4
V: Portal protein
W: Peptidoglycan hydrolase gp4
X: Portal protein


Theoretical massNumber of molelcules
Total (without water)1,048,17224
Polymers1,048,17224
Non-polymers00
Water00
1


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

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Components

#1: Protein
Peptidoglycan hydrolase gp4 / Gene product 4 / Gp4 / Internal virion protein gp4 / Tail adapter protein gp4


Mass: 16231.166 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26746
#2: Protein
Portal protein / Gene product 1 / Gp1 / Head-to-tail connector


Mass: 71116.539 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26744
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 the in-situ gp1-gp4 complex from bacteriophgage 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73420 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00373140
ELECTRON MICROSCOPYf_angle_d0.51999192
ELECTRON MICROSCOPYf_dihedral_angle_d3.8629828
ELECTRON MICROSCOPYf_chiral_restr0.04110716
ELECTRON MICROSCOPYf_plane_restr0.00313116

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