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- PDB-6b23: Capsid protein and C-terminal part of CpmB protein in the Staphyl... -

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Basic information

Entry
Database: PDB / ID: 6b23
TitleCapsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid
Components
  • Capsid morphogenesis B protein
  • Major head protein
KeywordsVIRUS / major capsid protein / HK97-like fold / scaffolding protein / procapsid
Function / homologyPathogenicity island protein gp6, Staphylococcus / Pathogenicity island protein gp6 superfamily / Pathogenicity island protein gp6 in Staphylococcus / Phage capsid / Phage capsid family / molecular adaptor activity / Major capsid protein / Hypothetical mobile element-associated protein
Function and homology information
Biological speciesStaphylococcus phage 80alpha (virus)
Staphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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)R01 AI083255 United States
CitationJournal: Elife / Year: 2017
Title: Competing scaffolding proteins determine capsid size during mobilization of pathogenicity islands.
Authors: Altaira D Dearborn / Erin A Wall / James L Kizziah / Laura Klenow / Laura K Parker / Keith A Manning / Michael S Spilman / John M Spear / Gail E Christie / Terje Dokland /
Abstract: pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the ... pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the helper's assembly pathway to form small capsids that can only accommodate the smaller SaPI1 genome, but not a complete phage genome. SaPI1 encodes two proteins, CpmA and CpmB, that are responsible for this size redirection. We have determined the structures of the 80α and SaPI1 procapsids to near-atomic resolution by cryo-electron microscopy, and show that CpmB competes with the 80α scaffolding protein (SP) for a binding site on the capsid protein (CP), and works by altering the angle between capsomers. We probed these interactions genetically and identified second-site suppressors of lethal mutations in SP. Our structures show, for the first time, the detailed interactions between SP and CP in a bacteriophage, providing unique insights into macromolecular assembly processes.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Structure summary / Category: citation / em_entity_assembly / Item: _citation.title / _em_entity_assembly.entity_id_list
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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 / database_2 / pdbx_struct_oper_list / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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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  • Superimposition on EM map
  • EMDB-7035
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major head protein
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein


Theoretical massNumber of molelcules
Total (without water)180,5128
Polymers180,5128
Non-polymers00
Water0
1
A: Major head protein
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,830,748480
Polymers10,830,748480
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
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein
x 5


  • icosahedral pentamer
  • 903 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)902,56240
Polymers902,56240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major head protein
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein
x 6


  • icosahedral 23 hexamer
  • 1.08 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,083,07548
Polymers1,083,07548
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 / Capsid protein


Mass: 36846.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 80alpha (virus) / Gene: orf47 / Production host: Staphylococcus aureus (bacteria) / Strain (production host): RN4220 / References: UniProt: A4ZFB3
#2: Protein
Capsid morphogenesis B protein


Mass: 8281.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ERS072840_02265 / Production host: Staphylococcus aureus (bacteria) / Strain (production host): ST63 / References: UniProt: O54465

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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: Lysogenic 80alpha with small terminase / Type: VIRUS
Details: Lysogenic 80alpha with small terminase gene deletion
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 10.81 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Source (recombinant)Organism: Staphylococcus aureus (bacteria) / Strain: RN4220
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Staphylococcus aureus
Virus shellName: ProcapsidCapsid / Diameter: 546 nm / Triangulation number (T number): 7
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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14087 / Symmetry type: POINT
RefinementResolution: 3.7→3.7 Å / Cor.coef. Fo:Fc: 0.864 / SU B: 61.235 / SU ML: 0.676 / ESU R: 0.644
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.4199 --
obs0.4199 98552 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: 238.756 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å21.53 Å25.05 Å2
2---4.46 Å21.12 Å2
3---6.23 Å2
Refinement stepCycle: 1 / Total: 9854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0210020
ELECTRON MICROSCOPYr_bond_other_d0.0010.029716
ELECTRON MICROSCOPYr_angle_refined_deg1.0021.96613488
ELECTRON MICROSCOPYr_angle_other_deg0.845322478
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.55651224
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.08426.208480
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.303151934
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.3171532
ELECTRON MICROSCOPYr_chiral_restr0.0610.21500
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0211252
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022148
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_it3.06623.8884920
ELECTRON MICROSCOPYr_mcbond_other3.06623.8884919
ELECTRON MICROSCOPYr_mcangle_it5.57835.8276136
ELECTRON MICROSCOPYr_mcangle_other5.57735.8276137
ELECTRON MICROSCOPYr_scbond_it2.31524.1545100
ELECTRON MICROSCOPYr_scbond_other2.31424.1545101
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.59536.1637353
ELECTRON MICROSCOPYr_long_range_B_refined14.6235621
ELECTRON MICROSCOPYr_long_range_B_other14.6235622
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.76→3.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.577 7229 -
Rfree-0 -
obs--100 %

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