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- PDB-3izg: Bacteriophage T7 prohead shell EM-derived atomic model -

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Entry
Database: PDB / ID: 3izg
TitleBacteriophage T7 prohead shell EM-derived atomic model
ComponentsMajor capsid protein 10A
KeywordsVIRUS / bacteriophage / capsid maturation / cryoelectron microscopy / morphogenetic intermediate / icosahedral
Function / homologyCapsid Gp10A/Gp10B / : / Major capsid protein / viral capsid / viral translational frameshifting / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.9 Å
AuthorsIonel, A. / Velazquez-Muriel, J.A. / Agirrezabala, X. / Luque, D. / Cuervo, A. / Caston, J.R. / Valpuesta, J.M. / Martin-Benito, J. / Carrascosa, J.L.
Citation
Journal: J Biol Chem / Year: 2011
Title: Molecular rearrangements involved in the capsid shell maturation of bacteriophage T7.
Authors: Alina Ionel / Javier A Velázquez-Muriel / Daniel Luque / Ana Cuervo / José R Castón / José M Valpuesta / Jaime Martín-Benito / José L Carrascosa /
Abstract: Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for ...Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for infecting a host under challenging environmental conditions. Here, we determine the mature capsid structure of T7 at 1 nm resolution by cryo-electron microscopy and compare it with the prohead to reveal the molecular basis of T7 shell maturation. The mature capsid presents an expanded and thinner shell, with a drastic rearrangement of the major protein monomers that increases in their interacting surfaces, in turn resulting in a new bonding lattice. The rearrangements include tilting, in-plane rotation, and radial expansion of the subunits, as well as a relative bending of the A- and P-domains of each subunit. The unique features of this shell transformation, which does not employ the accessory proteins, inserted domains, or molecular interactions observed in other phages, suggest a simple capsid assembling strategy that may have appeared early in the evolution of these viruses.
#1: Journal: Structure / Year: 2007
Title: Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
Authors: Xabier Agirrezabala / Javier A Velázquez-Muriel / Paulino Gómez-Puertas / Sjors H W Scheres / José M Carazo / José L Carrascosa /
Abstract: The existence of similar folds among major structural subunits of viral capsids has shown unexpected evolutionary relationships suggesting common origins irrespective of the capsids' host life domain. ...The existence of similar folds among major structural subunits of viral capsids has shown unexpected evolutionary relationships suggesting common origins irrespective of the capsids' host life domain. Tailed bacteriophages are emerging as one such family, and we have studied the possible existence of the HK97-like fold in bacteriophage T7. The procapsid structure at approximately 10 A resolution was used to obtain a quasi-atomic model by fitting a homology model of the T7 capsid protein gp10 that was based on the atomic structure of the HK97 capsid protein. A number of fold similarities, such as the fitting of domains A and P into the L-shaped procapsid subunit, are evident between both viral systems. A different feature is related to the presence of the amino-terminal domain of gp10 found at the inner surface of the capsid that might play an important role in the interaction of capsid and scaffolding proteins.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Feb 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
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A


Theoretical massNumber of molelcules
Total (without water)256,1277
Polymers256,1277
Non-polymers00
Water00
1
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A
x 60


Theoretical massNumber of molelcules
Total (without water)15,367,643420
Polymers15,367,643420
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
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A
x 5


  • icosahedral pentamer
  • 1.28 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,280,63735
Polymers1,280,63735
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A
x 6


  • icosahedral 23 hexamer
  • 1.54 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,536,76442
Polymers1,536,76442
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 capsid protein 10A


Mass: 36589.625 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T7 (virus) / References: UniProt: P19726

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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 T7 prohead / Type: VIRUS / Details: gp10A
Details of virusHost category: BACTERIA / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionName: 50mM Tris-HCl pH7.7 10mM MgCl2 100mM NaCl / pH: 7.7 / Details: 50mM Tris-HCl pH7.7 10mM MgCl2 100mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 carbon grids
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51600 X / Nominal defocus max: 1000 nm / Nominal defocus min: 3000 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: Wiener filter, defocus groups
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Spider / Resolution: 10.9 Å / Num. of particles: 4460 / Actual pixel size: 2.72 Å / Symmetry type: POINT
Atomic model buildingPDB-ID: 3E8K

3e8k


Accession code: 3E8K / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms12831 0 0 0 12831

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