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- PDB-2xyy: De Novo model of Bacteriophage P22 procapsid coat protein -

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Basic information

Entry
Database: PDB / ID: 2xyy
TitleDe Novo model of Bacteriophage P22 procapsid coat protein
ComponentsCOAT PROTEIN
KeywordsVIRUS / ICOSAHEDRAL RECONSTRUCTION
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 / Major capsid protein
Function and homology information
Biological speciesENTEROBACTERIA PHAGE P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G
AuthorsChen, D.-H. / Baker, M.L. / Hryc, C.F. / DiMaio, F. / Jakana, J. / Wu, W. / Dougherty, M. / Haase-Pettingell, C. / Schmid, M.F. / Jiang, W. ...Chen, D.-H. / Baker, M.L. / Hryc, C.F. / DiMaio, F. / Jakana, J. / Wu, W. / Dougherty, M. / Haase-Pettingell, C. / Schmid, M.F. / Jiang, W. / Baker, D. / King, J.A. / Chiu, W.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.
Authors: Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / ...Authors: Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / Jonathan A King / Wah Chiu /
Abstract: Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This ...Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This process, conserved among dsDNA viruses such as herpes viruses and bacteriophages, is key to forming infectious virions. Bacteriophage P22 has served as a model system for this study in the past several decades. However, how capsid assembly is initiated, where and how scaffolding proteins bind to coat proteins in the procapsid, and the conformational changes upon capsid maturation still remain elusive. Here, we report Cα backbone models for the P22 procapsid and infectious virion derived from electron cryomicroscopy density maps determined at 3.8- and 4.0-Å resolution, respectively, and the first procapsid structure at subnanometer resolution without imposing symmetry. The procapsid structures show the scaffolding protein interacting electrostatically with the N terminus (N arm) of the coat protein through its C-terminal helix-loop-helix motif, as well as unexpected interactions between 10 scaffolding proteins and the 12-fold portal located at a unique vertex. These suggest a critical role for the scaffolding proteins both in initiating the capsid assembly at the portal vertex and propagating its growth on a T = 7 icosahedral lattice. Comparison of the procapsid and the virion backbone models reveals coordinated and complex conformational changes. These structural observations allow us to propose a more detailed molecular mechanism for the scaffolding-mediated capsid assembly initiation including portal incorporation, release of scaffolding proteins upon DNA packaging, and maturation into infectious virions.
History
DepositionNov 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id

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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
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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-1824
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  • Superimposition on EM map
  • EMDB-1824
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)327,5697
Polymers327,5697
Non-polymers00
Water0
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)19,654,157420
Polymers19,654,157420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
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
point symmetry operation5
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
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
point symmetry operation6
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
COAT PROTEIN / P22 / Coordinate model: Cα atoms only


Mass: 46795.613 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE P22 (virus)
Production host: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain (production host): DB7136 / Variant (production host): 13AMH101 / References: UniProt: A8CGC7, UniProt: P26747*PLUS

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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: BACTERIOPHAGE P22 PROCAPSID / Type: VIRUS / Details: BAD MICROGRAPHS WERE EXCLUDED VISUALLY
Buffer solutionName: 50 MM TRIS PH 7.6, 25 MM NACL, 2MM EDTA / pH: 7.6 / Details: 50 MM TRIS PH 7.6, 25 MM NACL, 2MM EDTA
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: VITRIFICATION 1 - CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 4.2, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

MicroscopyModel: JEOL KYOTO-3000SFF / Date: Mar 7, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Calibrated magnification: 60000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 500 nm / Cs: 1.6 mm
Specimen holderTemperature: 4.2 K
Image recordingElectron dose: 36 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 921

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Processing

EM softwareName: EMAN / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: FOURIER METHODS / Resolution: 3.8 Å / Num. of particles: 23400 / Nominal pixel size: 1.06 Å / Actual pixel size: 1.06 Å
Details: MAKE3D IN EMAN.N-TERMINAL 9 RESIDUES AND C-TERMINAL 5 RESIDUES WERE NOT MODELED.SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1824.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: FSC / Details: REFINEMENT PROTOCOL--EM
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 0 0 2912

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