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- PDB-6qym: The cryo-EM structure of the connector of the genome empited bact... -

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Entry
Database: PDB / ID: 6qym
TitleThe cryo-EM structure of the connector of the genome empited bacteriophage phi29
ComponentsPortal protein
KeywordsVIRUS / bacteriophage / phi29 / prohead
Function / homologyPortal protein Gp10 superfamily / Portal protein Gp10 / Phage Connector (GP10) / viral portal complex / viral DNA genome packaging / viral genome ejection through host cell envelope, short tail mechanism / viral procapsid / RNA binding / Portal protein
Function and homology information
Biological speciesBacillus phage phi29 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXu, J. / Wang, D. / Gui, M. / Xiang, Y.
Funding supportChina , 3件
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100China
Ministry of Science and Technology (China)2015CB910102China
National Natural Science Foundation of China31470721China
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 9, 2019 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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Assembly

Deposited unit
0a: Portal protein
0b: Portal protein
0c: Portal protein
0d: Portal protein
0e: Portal protein
0f: Portal protein
0g: Portal protein
0h: Portal protein
0i: Portal protein
0j: Portal protein
0k: Portal protein
0l: Portal protein


Theoretical massNumber of molelcules
Total (without water)431,00812
Polymers431,00812
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Portal protein / Connector protein / Gene product 10 / gp10 / Gene product 19 / gp19 / Head-to-tail connector / Probable portal protein / Protein p10 / Upper collar protein


Mass: 35917.293 Da / Num. of mol.: 12
Details: The residues from 285 to 301 are assigned Alanines due to the poor quality of density map.
Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (bacteriophage) / References: UniProt: P04332

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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: 1 / Source: NATURAL
Source (natural)Organism: Bacillus phage phi29 (bacteriophage)
Details of virusEmpty: YES / 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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37761 / Symmetry type: POINT

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