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- PDB-8eap: Cryo-EM structure of the in-situ gp10-gp26 from bacteriophage P22 -

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Basic information

Entry
Database: PDB / ID: 8eap
TitleCryo-EM structure of the in-situ gp10-gp26 from bacteriophage P22
Components
  • Packaged DNA stabilization protein gp10
  • Tail needle protein gp26
KeywordsVIRAL PROTEIN / Bacteriophage P22
Function / homologyBacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / symbiont genome entry into host cell via pore formation in plasma membrane / Packaged DNA stabilization protein gp10 / Tail needle protein gp26
Function and homology information
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Tail needle protein gp26
A: Tail needle protein gp26
C: Tail needle protein gp26
G: Packaged DNA stabilization protein gp10
H: Packaged DNA stabilization protein gp10
I: Packaged DNA stabilization protein gp10
E: Packaged DNA stabilization protein gp10
D: Packaged DNA stabilization protein gp10
F: Packaged DNA stabilization protein gp10


Theoretical massNumber of molelcules
Total (without water)334,0389
Polymers334,0389
Non-polymers00
Water00
1


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

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Components

#1: Protein Tail needle protein gp26 / Head completion protein / Packaged DNA stabilization protein / Tail accessory factor gp26


Mass: 6524.245 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P35837
#2: 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 gp10-gp26 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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106070 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324498
ELECTRON MICROSCOPYf_angle_d0.43633186
ELECTRON MICROSCOPYf_dihedral_angle_d4.1273420
ELECTRON MICROSCOPYf_chiral_restr0.0433612
ELECTRON MICROSCOPYf_plane_restr0.0034326

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