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- PDB-6qyz: The cryo-EM structure of prohead RNA in bacteriophage phi29 prohead -

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Basic information

Entry
Database: PDB / ID: 6qyz
TitleThe cryo-EM structure of prohead RNA in bacteriophage phi29 prohead
Componentsthe prohead RNA (71-MER) in bacteriophage phi29
KeywordsVIRUS / bacteriophage / phi29 / prohead
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesBacillus phage phi29 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsXu, J. / Wang, D. / Gui, M. / Xiang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 China
Ministry of Science and Technology (China)2015CB910102 China
National Natural Science Foundation of China31470721 China
CitationJournal: Nat Commun / Year: 2019
Title: Structural assembly of the tailed bacteriophage ϕ29.
Authors: Jingwei Xu / Dianhong Wang / Miao Gui / Ye Xiang /
Abstract: The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile ...The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.
History
DepositionMar 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Other
Category: atom_sites / em_image_scans / em_single_particle_entity
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
D: the prohead RNA (71-MER) in bacteriophage phi29
A: the prohead RNA (71-MER) in bacteriophage phi29
B: the prohead RNA (71-MER) in bacteriophage phi29
C: the prohead RNA (71-MER) in bacteriophage phi29
E: the prohead RNA (71-MER) in bacteriophage phi29


Theoretical massNumber of molelcules
Total (without water)192,0935
Polymers192,0935
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-20 kcal/mol
Surface area52130 Å2
MethodPISA

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Components

#1: RNA chain
the prohead RNA (71-MER) in bacteriophage phi29


Mass: 38418.578 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (virus)

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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: Bacillus phage phi29 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus phage phi29 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6472 / Symmetry type: POINT

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