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- PDB-6omc: capsid of T5 virion -

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Basic information

Entry
Database: PDB / ID: 6omc
Titlecapsid of T5 virion
ComponentsMajor capsid protein
KeywordsVIRUS / capsid / HK97-fold / dsDNA-phage / icosahedral
Function / homologyviral scaffold / T=13 icosahedral viral capsid / : / Phage capsid / Phage capsid family / symbiont-mediated evasion of host immune response / viral capsid / Major capsid protein
Function and homology information
Biological speciesEscherichia phage T5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHuet, A. / Duda, R.L. / Boulanger, P. / Conway, J.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM047795 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10 OD019995 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy.
Authors: Alexis Huet / Robert L Duda / Pascale Boulanger / James F Conway /
Abstract: The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a ...The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 Å for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 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
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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-20125
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)428,10813
Polymers428,10813
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)25,686,460780
Polymers25,686,460780
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
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
x 5


  • icosahedral pentamer
  • 2.14 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)2,140,53865
Polymers2,140,53865
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.57 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)2,568,64678
Polymers2,568,64678
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 / Capsid protein pb8 / Major head protein


Mass: 32931.359 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGD8

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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: Escherichia phage T5 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 100 MDa / Experimental value: NO
Source (natural)Organism: Escherichia phage T5 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Escherichia coli
Virus shellName: full-head / Diameter: 900 nm / Triangulation number (T number): 13
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium chlorideNaCl1
210 mMTris1
31 mMMGCl21
41 mMCaCL21
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3523

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Processing

EM software
IDNameCategory
1X3Dparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9UCSF Chimeramodel refinement
10MDFFmodel refinement
11PHENIXmodel refinement
12Auto3DEMinitial Euler assignment
13Auto3DEMfinal Euler assignment
15Auto3DEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 29997
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18901 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 2FT1

2ft1


Accession code: 2FT1 / Source name: PDB / Type: experimental model

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