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- PDB-1foq: PENTAMERIC MODEL OF THE BACTERIOPHAGE PHI29 PROHEAD RNA -

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Entry
Database: PDB / ID: 1foq
TitlePENTAMERIC MODEL OF THE BACTERIOPHAGE PHI29 PROHEAD RNA
ComponentsBACTERIOPHAGE PHI29 PROHEAD RNA
KeywordsRNA / dsRNA oligomeric model / Prohead RNA / Bacteriophage phi29
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesBacillus phage phi29 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsSimpson, A.A. / Tao, Y. / Leiman, P.G. / Badasso, M.O. / He, Y. / Jardine, P.J. / Olson, N.H. / Morais, M.C. / Grimes, S. / Anderson, D.L. ...Simpson, A.A. / Tao, Y. / Leiman, P.G. / Badasso, M.O. / He, Y. / Jardine, P.J. / Olson, N.H. / Morais, M.C. / Grimes, S. / Anderson, D.L. / Baker, T.S. / Rossmann, M.G.
CitationJournal: Nature / Year: 2000
Title: Structure of the bacteriophage phi29 DNA packaging motor.
Authors: A A Simpson / Y Tao / P G Leiman / M O Badasso / Y He / P J Jardine / N H Olson / M C Morais / S Grimes / D L Anderson / T S Baker / M G Rossmann /
Abstract: Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we ...Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we describe the motor that packages the double-stranded DNA of the Bacillus subtilis bacteriophage phi29 into a precursor capsid. We determined the structure of the head-tail connector--the central component of the phi29 DNA packaging motor--to 3.2 A resolution by means of X-ray crystallography. We then fitted the connector into the electron densities of the prohead and of the partially packaged prohead as determined using cryo-electron microscopy and image reconstruction analysis. Our results suggest that the prohead plus dodecameric connector, prohead RNA, viral ATPase and DNA comprise a rotary motor with the head-prohead RNA-ATPase complex acting as a stator, the DNA acting as a spindle, and the connector as a ball-race. The helical nature of the DNA converts the rotary action of the connector into translation of the DNA.
History
DepositionAug 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Data processing / Other
Category: atom_sites / cell ...atom_sites / cell / em_3d_reconstruction / 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[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 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Mar 5, 2025Group: Data processing / Structure summary / Category: em_3d_reconstruction / pdbx_entry_details

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Assembly

Deposited unit
A: BACTERIOPHAGE PHI29 PROHEAD RNA
B: BACTERIOPHAGE PHI29 PROHEAD RNA
C: BACTERIOPHAGE PHI29 PROHEAD RNA
D: BACTERIOPHAGE PHI29 PROHEAD RNA
E: BACTERIOPHAGE PHI29 PROHEAD RNA


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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain
BACTERIOPHAGE PHI29 PROHEAD RNA


Mass: 38418.578 Da / Num. of mol.: 5 / Fragment: 1-120 BASE FRAGMENT
Mutation: BASES 5, 18-20, 106, 109 AND 118-120 ARE NOT IN THE MODEL
Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / References: EMBL: X05973
Has protein modificationN

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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 Phi29 tailed virus / Type: VIRUS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
pH: 7.5 / Method: other
Details: This particular structure is not described in this paper.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC FILM

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Processing

3D reconstructionResolution: 20 Å
RefinementHighest resolution: 20 Å
Refinement stepCycle: LAST / Highest resolution: 20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 12105 0 0 12105

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