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- PDB-7rwz: SaPIbov5 procapsid structure including size redirecting protein Ccm -

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Basic information

Entry
Database: PDB / ID: 7rwz
TitleSaPIbov5 procapsid structure including size redirecting protein Ccm
Components
  • Cos capsid morphogenesis protein (Ccm)
  • Major capsid protein
KeywordsVIRUS / HK97-like fold / capsid size redirection / major capsid protein
Function / homology
Function and homology information


ATP-dependent peptidase activity / membrane => GO:0016020 / serine-type endopeptidase activity
Similarity search - Function
Phage capsid / Phage capsid family / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit / Phage capsid protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsHawkins, N.C. / Kizziah, J.L. / Dokland, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI132977 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: Nat Commun / Year: 2021
Title: Shape shifter: redirection of prolate phage capsid assembly by staphylococcal pathogenicity islands.
Authors: N'Toia C Hawkins / James L Kizziah / José R Penadés / Terje Dokland /
Abstract: Staphylococcus aureus pathogenicity islands (SaPIs) are molecular parasites that hijack helper phages for their transfer. SaPIbov5, the prototypical member of a family of cos type SaPIs, redirects ...Staphylococcus aureus pathogenicity islands (SaPIs) are molecular parasites that hijack helper phages for their transfer. SaPIbov5, the prototypical member of a family of cos type SaPIs, redirects the assembly of ϕ12 helper capsids from prolate to isometric. This size and shape shift is dependent on the SaPIbov5-encoded protein Ccm, a homolog of the ϕ12 capsid protein (CP). Using cryo-electron microscopy, we have determined structures of prolate ϕ12 procapsids and isometric SaPIbov5 procapsids. ϕ12 procapsids have icosahedral end caps with T = 4 architecture and a T = 14 cylindrical midsection, whereas SaPIbov5 procapsids have T = 4 icosahedral architecture. We built atomic models for CP and Ccm, and show that Ccm occupies the pentameric capsomers in the isometric SaPIbov5 procapsids, suggesting that preferential incorporation of Ccm pentamers prevents the cylindrical midsection from forming. Our results highlight that pirate elements have evolved diverse mechanisms to suppress phage multiplication, including the acquisition of phage capsid protein homologs.
History
DepositionAug 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 17, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-24720
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  • Superimposition on EM map
  • EMDB-24720
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cos capsid morphogenesis protein (Ccm)
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)176,3474
Polymers176,3474
Non-polymers00
Water00
1
A: Cos capsid morphogenesis protein (Ccm)
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,580,794240
Polymers10,580,794240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cos capsid morphogenesis protein (Ccm)
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
x 5


  • icosahedral pentamer
  • 882 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)881,73320
Polymers881,73320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Cos capsid morphogenesis protein (Ccm)
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.06 MDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)1,058,07924
Polymers1,058,07924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Cos capsid morphogenesis protein (Ccm)


Mass: 40468.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) / References: UniProt: E2FZQ5
#2: Protein Major capsid protein


Mass: 45292.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) / References: UniProt: A0A7H9CBC0
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: SaPIbov5 procapsid / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7.8
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: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14rc1_3161: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28566 / Symmetry type: POINT

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