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- PDB-6qxm: Cryo-EM structure of T7 bacteriophage portal protein, 12mer, open... -

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Basic information

Entry
Database: PDB / ID: 6qxm
TitleCryo-EM structure of T7 bacteriophage portal protein, 12mer, open valve
ComponentsPortal protein
KeywordsVIRAL PROTEIN / DNA packaging
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsFabrega-Ferrer, M. / Cuervo, A. / Machon, C. / Fernandez, F.J. / Perez-Luque, R. / Pous, J. / Vega, M.C. / Carrascosa, J.L. / Coll, M.
Funding support Spain, 7items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU 2014-54181 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEV-2013-0347 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2011-09071 Spain
European Commission653706
CitationJournal: Nat Commun / Year: 2019
Title: Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism.
Authors: Ana Cuervo / Montserrat Fàbrega-Ferrer / Cristina Machón / José Javier Conesa / Francisco J Fernández / Rosa Pérez-Luque / Mar Pérez-Ruiz / Joan Pous / M Cristina Vega / José L Carrascosa / Miquel Coll /
Abstract: Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been ...Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites / cell
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
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
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein


Theoretical massNumber of molelcules
Total (without water)725,50112
Polymers725,50112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76710 Å2
ΔGint-366 kcal/mol
Surface area204690 Å2
MethodPISA

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Components

#1: Protein
Portal protein / Gene product 8 / Gp8 / Head-to-tail connector


Mass: 60458.387 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03728

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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 packaging protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Enterobacteria phage T7 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
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: 39.4 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32688 / Symmetry type: POINT

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