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- PDB-2xvr: Phage T7 empty mature head shell -

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Basic information

Entry
Database: PDB / ID: 2xvr
TitlePhage T7 empty mature head shell
ComponentsMAJOR CAPSID PROTEIN 10A
KeywordsVIRUS / CAPSID MATURATION / MORPHOGENETIC INTERMEDIATE
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: 10.8 Å
AuthorsIonel, A. / Velazquez-Muriel, J.A. / Luque, D. / Cuervo, A. / Caston, J.R. / Valpuesta, J.M. / Martin-Benito, J. / Carrascosa, J.L.
CitationJournal: 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.
History
DepositionOct 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other / Version format compliance
Revision 1.2Mar 20, 2013Group: Other / Refinement description
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_image_scans
Revision 1.4Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id / _em_software.name
Revision 1.5May 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

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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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-1810
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1810
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-1810
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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
G: MAJOR CAPSID PROTEIN 10A


Theoretical massNumber of molelcules
Total (without water)256,1277
Polymers256,1277
Non-polymers00
Water00
1
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
G: 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
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
G: 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
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
G: 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 / BACTERIOPHAGE T7


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: PHAGE T7 EMPTY HEAD / Type: VIRUS
Buffer solutionName: 50 MM TRIS-HCL, PH 7.8, 10 MM MGCL2, 0.1 M NACL / pH: 7.8 / Details: 50 MM TRIS-HCL, PH 7.8, 10 MM MGCL2, 0.1 M NACL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: VITRIFICATION 1 -- CRYOGEN- ETHANE,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: Xmipp / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 10.8 Å / Num. of particles: 5100 / Actual pixel size: 1.4 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1810. (DEPOSITION ID: 7638).
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 1OHG

1ohg


Accession code: 1OHG / Source name: PDB / Type: experimental model
RefinementHighest resolution: 10.8 Å
Refinement stepCycle: LAST / Highest resolution: 10.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12831 0 0 0 12831

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