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- PDB-6c22: Capsid protein in the Staphylococcus aureus phage 80alpha-derived... -

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Basic information

Entry
Database: PDB / ID: 6c22
TitleCapsid protein in the Staphylococcus aureus phage 80alpha-derived SaPI1 mature capsid
ComponentsMajor head protein
KeywordsVIRUS / major capsid protein / HK97-like fold / mature capsid
Function / homologyPhage capsid / Phage capsid family / Major capsid protein
Function and homology information
Biological speciesStaphylococcus virus 80alpha
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsKizziah, J.L. / Dearborn, A.D. / Dokland, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI083255 United States
CitationJournal: Viruses / Year: 2017
Title: Cleavage and Structural Transitions during Maturation of Staphylococcus aureus Bacteriophage 80α and SaPI1 Capsids.
Authors: James L Kizziah / Keith A Manning / Altaira D Dearborn / Erin A Wall / Laura Klenow / Rosanne L L Hill / Michael S Spilman / Scott M Stagg / Gail E Christie / Terje Dokland /
Abstract: In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of ...In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of the major capsid protein (CP) and other capsid-associated proteins, including the scaffolding protein (SP) that serves as a chaperone for the assembly process. bacteriophage 80α is capable of high frequency mobilization of mobile genetic elements called pathogenicity islands (SaPIs), such as SaPI1. SaPI1 redirects the assembly pathway of 80α to form capsids that are smaller than those normally made by the phage alone. Both CP and SP of 80α are N-terminally processed by a host-encoded protease, Prp. We have analyzed phage mutants that express pre-cleaved or uncleavable versions of CP or SP, and show that the N-terminal sequence in SP is absolutely required for assembly, but does not need to be cleaved in order to produce viable capsids. Mutants with pre-cleaved or uncleavable CP display normal viability. We have used cryo-EM to solve the structures of mature capsids from an 80α mutant expressing uncleavable CP, and from wildtype SaPI1. Comparisons with structures of 80α and SaPI1 procapsids show that capsid maturation involves major conformational changes in CP, consistent with a release of the CP N-arm by SP. The hexamers reorganize during maturation to accommodate the different environments in the 80α and SaPI1 capsids.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / refine
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-7333
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein


Theoretical massNumber of molelcules
Total (without water)147,3884
Polymers147,3884
Non-polymers00
Water0
1
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
x 60


Theoretical massNumber of molelcules
Total (without water)8,843,252240
Polymers8,843,252240
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: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
x 5


  • icosahedral pentamer
  • 737 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)736,93820
Polymers736,93820
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
x 6


  • icosahedral 23 hexamer
  • 884 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)884,32524
Polymers884,32524
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
Major head protein


Mass: 36846.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus virus 80alpha / Cell line (production host): RN4220 / Production host: Staphylococcus aureus (bacteria) / Strain (production host): ST65 / References: UniProt: A4ZFB3

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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: Staphylococcus phage 80alpha / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 8.83 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Source (recombinant)Organism: Staphylococcus aureus (bacteria) / Strain: RN4220
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Staphylococcus aureus
Virus shellName: Capsid / Diameter: 460 nm / Triangulation number (T number): 4
Buffer solutionpH: 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: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 62000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN1.9particle selection
4EMAN1.9CTF correction
7UCSF Chimera1.10.2model fitting
9REFMAC5.8.0158model refinement
10Coot0.8.8model refinement
11Coot0.8.6.1model refinementWinCoot (Windows version of Coot)
12Auto3DEM4.01initial Euler assignment
13Auto3DEM4.01final Euler assignment
14Auto3DEM4.01classification
15Auto3DEM4.013D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 6471
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6471 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementResolution: 8.4→8.4 Å / Cor.coef. Fo:Fc: 0.898 / SU B: 421.503 / SU ML: 2.971
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.32913 --
obs0.32913 8480 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 177.942 Å2
Baniso -1Baniso -2Baniso -3
1--18.44 Å20.93 Å2-5.31 Å2
2---10.43 Å26.86 Å2
3---28.88 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0195464
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.0641.9447604
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg1.71451096
ELECTRON MICROSCOPYr_dihedral_angle_2_deg4.434204
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.395154
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0520.21036
ELECTRON MICROSCOPYr_gen_planes_refined0.0010.024416
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.43528.6154396
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it0.82942.9215488
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it0.08928.5561068
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined5.52417403
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 8→8.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.452 638 -
Rfree-0 -
obs--100 %

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