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- PDB-7jw1: Satellite phage P4 procapsid including size determination (Sid) p... -

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Basic information

Entry
Database: PDB / ID: 7jw1
TitleSatellite phage P4 procapsid including size determination (Sid) protein
Components
  • Major capsid protein gpN
  • Size determination protein Sid
KeywordsVIRUS / bacteriophage / phage / procapsid / satellite phage / size determination / capsid protein / molecular piracy
Function / homologyBacteriophage P2, capsid / Phage major capsid protein, P2 family / viral capsid / Glycoprotein 3 / Capsid proteins
Function and homology information
Biological speciesEscherichia phage P2 (virus)
Enterobacteria phage P4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsKizziah, J.L. / Dokland, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: Viruses / Year: 2020
Title: Structure of the Capsid Size-Determining Scaffold of "Satellite" Bacteriophage P4.
Authors: James L Kizziah / Cynthia M Rodenburg / Terje Dokland /
Abstract: P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the ...P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the original example of what we have termed "molecular piracy", the process by which one MGE usurps the life cycle of another for its own propagation. The P2 helper provides most of the structural gene products for assembly of the P4 virion. However, when P4 is mobilized by P2, the resulting capsids are smaller than those normally formed by P2 alone. The P4-encoded protein responsible for this size change is called Sid, which forms an external scaffolding cage around the P4 procapsids. We have determined the high-resolution structure of P4 procapsids, allowing us to build an atomic model for Sid as well as the gpN capsid protein. Sixty copies of Sid form an intertwined dodecahedral cage around the = 4 procapsid, making contact with only one out of the four symmetrically non-equivalent copies of gpN. Our structure provides a basis for understanding the mutants in gpN that prevent small capsid formation, as well as the "super-sid" mutations that counteract the effect of the mutations, and suggests a model for capsid size redirection by Sid.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Assembly

Deposited unit
A: Major capsid protein gpN
B: Major capsid protein gpN
C: Major capsid protein gpN
D: Major capsid protein gpN
E: Size determination protein Sid
a: Major capsid protein gpN
b: Major capsid protein gpN
c: Major capsid protein gpN
d: Major capsid protein gpN
e: Size determination protein Sid


Theoretical massNumber of molelcules
Total (without water)376,92610
Polymers376,92610
Non-polymers00
Water00
1
A: Major capsid protein gpN
B: Major capsid protein gpN
C: Major capsid protein gpN
D: Major capsid protein gpN
E: Size determination protein Sid
a: Major capsid protein gpN
b: Major capsid protein gpN
c: Major capsid protein gpN
d: Major capsid protein gpN
e: Size determination protein Sid
x 30


Theoretical massNumber of molelcules
Total (without water)11,307,765300
Polymers11,307,765300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation29
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major capsid protein gpN / GpN


Mass: 40291.484 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage P2 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P25477
#2: Protein Size determination protein Sid / Capsid size determination protein


Mass: 27296.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P4 (virus) / Gene: sid / Production host: Escherichia coli (E. coli) / References: UniProt: P05461
Has protein modificationY

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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: P4 procapsid / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.4
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
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 438018 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00369366
ELECTRON MICROSCOPYf_angle_d0.51593666
ELECTRON MICROSCOPYf_dihedral_angle_d30.2939408
ELECTRON MICROSCOPYf_chiral_restr0.04210494
ELECTRON MICROSCOPYf_plane_restr0.00312186

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