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- PDB-3iyi: P22 expanded head coat protein structures reveal a novel mechanis... -

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Basic information

Entry
Database: PDB / ID: 3iyi
TitleP22 expanded head coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links
ComponentsP22 coat protein in procapsid shells
KeywordsVIRUS / HK97-like fold
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral procapsid / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsParent, K.N. / Khayat, R. / Tu, L.H. / Suhanovsky, M.M. / Cortines, J.R. / Teschke, C.M. / Johnson, J.E. / Baker, T.S.
CitationJournal: Structure / Year: 2010
Title: P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks.
Authors: Kristin N Parent / Reza Khayat / Long H Tu / Margaret M Suhanovsky / Juliana R Cortines / Carolyn M Teschke / John E Johnson / Timothy S Baker /
Abstract: Viral capsid assembly and stability in tailed, dsDNA phage and Herpesviridae are achieved by various means including chemical crosslinks (unique to HK97), or auxiliary proteins (lambda, T4, phi29, ...Viral capsid assembly and stability in tailed, dsDNA phage and Herpesviridae are achieved by various means including chemical crosslinks (unique to HK97), or auxiliary proteins (lambda, T4, phi29, and herpesviruses). All these viruses have coat proteins (CP) with a conserved, HK97-like core structure. We used a combination of trypsin digestion, gold labeling, cryo-electron microscopy, 3D image reconstruction, and comparative modeling to derive two independent, pseudoatomic models of bacteriophage P22 CP: before and after maturation. P22 capsid stabilization results from intersubunit interactions among N-terminal helices and an extensive "P loop," which obviate the need for crosslinks or auxiliary proteins. P22 CP also has a telokin-like Ig domain that likely stabilizes the monomer fold so that assembly may proceed via individual subunit addition rather than via preformed capsomers as occurs in HK97. Hence, the P22 CP structure may be a paradigm for understanding how monomers assemble in viruses like phi29 and HSV-1.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Jan 21, 2015Group: Database references
Revision 1.4Dec 7, 2016Group: Source and taxonomy
Revision 1.5Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.6Feb 21, 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 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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
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Structure viewerMolecule:
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Assembly

Deposited unit
A: P22 coat protein in procapsid shells
B: P22 coat protein in procapsid shells
C: P22 coat protein in procapsid shells
D: P22 coat protein in procapsid shells
E: P22 coat protein in procapsid shells
F: P22 coat protein in procapsid shells
G: P22 coat protein in procapsid shells


Theoretical massNumber of molelcules
Total (without water)327,5697
Polymers327,5697
Non-polymers00
Water00
1
A: P22 coat protein in procapsid shells
B: P22 coat protein in procapsid shells
C: P22 coat protein in procapsid shells
D: P22 coat protein in procapsid shells
E: P22 coat protein in procapsid shells
F: P22 coat protein in procapsid shells
G: P22 coat protein in procapsid shells
x 60


Theoretical massNumber of molelcules
Total (without water)19,654,157420
Polymers19,654,157420
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: P22 coat protein in procapsid shells
B: P22 coat protein in procapsid shells
C: P22 coat protein in procapsid shells
D: P22 coat protein in procapsid shells
E: P22 coat protein in procapsid shells
F: P22 coat protein in procapsid shells
G: P22 coat protein in procapsid shells
x 5


  • icosahedral pentamer
  • 1.64 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,637,84635
Polymers1,637,84635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: P22 coat protein in procapsid shells
B: P22 coat protein in procapsid shells
C: P22 coat protein in procapsid shells
D: P22 coat protein in procapsid shells
E: P22 coat protein in procapsid shells
F: P22 coat protein in procapsid shells
G: P22 coat protein in procapsid shells
x 6


  • icosahedral 23 hexamer
  • 1.97 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,965,41642
Polymers1,965,41642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


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

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Components

#1: Protein
P22 coat protein in procapsid shells / Protein gp5 / Coordinate model: Cα atoms only


Mass: 46795.613 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage P22 (virus) / References: UniProt: P26747

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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: P22 Procapsid Shell / Type: VIRUS
Details: Icosahedral. Scaffolding protein, portal and ejection proteins removed by 0.5 M GuHCl
Details of virusEmpty: YES / Enveloped: NO / Host category: BACTERIA(EUBACTERIA) / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Salmonella typhimurium
Buffer solutionName: 20 mM sodium phosphate buffer, pH = 7.6 / pH: 7.6 / Details: 20 mM sodium phosphate buffer, pH = 7.6
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20 mM sodium phosphate
Specimen supportDetails: Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 89 K / Humidity: 100 % / Method: Blot for 2-3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jan 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 3650 nm / Nominal defocus min: 410 nm / Cs: 2.3 mm / Astigmatism: at working magnification / Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Polrar Multi Specimen Holder / Temperature: 90 K / Temperature (max): 90 K / Temperature (min): 90 K / Tilt angle max: -9999 ° / Tilt angle min: -9999 °
Image recordingElectron dose: 8 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2MODELLERmodel fitting
3Auto3DEM3D reconstruction
CTF correctionDetails: ROBEM
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: iterative model-based procedure / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 11997 / Nominal pixel size: 1.62 Å / Actual pixel size: 1.62 Å
Details: ( Details about the particle: data were collected on film )
Symmetry type: POINT
Atomic model building
IDProtocolSpaceTarget criteriaDetails
1FLEXIBLE FITREALcross-correlation coefficientMETHOD--local refinement, flexible fitting REFINEMENT PROTOCOL--rigid body
2
Atomic model building

Source name: PDB / Type: experimental model

IDPDB-ID 3D fitting-IDAccession codeDetailsInitial refinement model-ID
11OHG

1ohg

11OHGhomology model based on 1OHG1
21FHG

1fhg

21FHGhomology model based on 1FHG2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 0 0 2688

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