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- PDB-2xd8: Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7 -

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Basic information

Entry
Database: PDB / ID: 2xd8
TitleCapsid structure of the infectious Prochlorococcus Cyanophage P-SSP7
ComponentsT7-LIKE CAPSID PROTEIN
KeywordsVIRUS / MARINE PODOVIRUS / T7-LIKE VIRUS
Function / homology: / Major capsid protein / T7-like capsid protein
Function and homology information
Biological speciesPROCHLOROCOCCUS PHAGE P-SSP7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G
AuthorsLiu, X. / Zhang, Q. / Murata, K. / Baker, M.L. / Sullivan, M.B. / Fu, C. / Dougherty, M. / Schmid, M.F. / Osburne, M.S. / Chisholm, S.W. / Chiu, W.
CitationJournal: Nat Struct Mol Biol / Year: 2010
Title: Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus.
Authors: Xiangan Liu / Qinfen Zhang / Kazuyoshi Murata / Matthew L Baker / Matthew B Sullivan / Caroline Fu / Matthew T Dougherty / Michael F Schmid / Marcia S Osburne / Sallie W Chisholm / Wah Chiu /
Abstract: Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo-electron microscopy yields icosahedral and asymmetrical structures of ...Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo-electron microscopy yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6-A and 9-A resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among five of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the 'valve' density in the nozzle, an orientation difference in the tail fibers, a disordering of the C terminus of the portal protein and the disappearance of the core proteins. In addition, cryo-electron tomography of P-SSP7 infecting Prochlorococcus showed the same tail-fiber conformation as that in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release.
History
DepositionApr 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other / Refinement description / Version format compliance
Revision 1.2Oct 3, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4May 8, 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
  • EMDB-1713
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)276,4597
Polymers276,4597
Non-polymers00
Water00
1
A: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)16,587,569420
Polymers16,587,569420
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: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 1.38 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,382,29735
Polymers1,382,29735
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 1.66 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,658,75742
Polymers1,658,75742
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
T7-LIKE CAPSID PROTEIN / GP10 / Coordinate model: Cα atoms only


Mass: 39494.211 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLOROCOCCUS PHAGE P-SSP7 (virus)
Description: P-SSP7 WERE PROPAGATED ON PROCHLOROCOCCUS MED4.
Production host: PROCHLOROCOCCUS MED4 (bacteria) / References: UniProt: Q58N30

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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: CYANOPHAGE P-SSP7 / Type: VIRUS
Buffer solutionName: 100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL / pH: 7.5 / Details: 100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL
SpecimenConc.: 5 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

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Aug 31, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 4.1 mm
Specimen holderTemperature: 101 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 1059
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: MPSA / Category: 3D reconstruction
CTF correctionDetails: INDIVIDUAL MICROGRAPH
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 4.6 Å / Num. of particles: 36000 / Nominal pixel size: 1.27 Å / Actual pixel size: 1.17 Å / Magnification calibration: 2D CRYSTAL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1713.
Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11IJG

1ijg

11IJG1PDBexperimental model
22JES

2jes

12JES2PDBexperimental model
RefinementHighest resolution: 4.6 Å
Refinement stepCycle: LAST / Highest resolution: 4.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 0 0 2541

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