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- PDB-3ja7: Cryo-EM structure of the bacteriophage T4 portal protein assembly... -

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Basic information

Entry
Database: PDB / ID: 3ja7
TitleCryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution
ComponentsPortal protein gp20
KeywordsVIRAL PROTEIN
Function / homologyPortal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral portal complex / viral genome packaging / viral release from host cell / host cell plasma membrane / membrane / Portal protein
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSun, L. / Zhang, X. / Gao, S. / Rao, P.A. / Padilla-Sanchez, V. / Chen, Z. / Sun, S. / Xiang, Y. / Subramaniam, S. / Rao, V.B. / Rossmann, M.G.
CitationJournal: Nat Commun / Year: 2015
Title: Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.
Authors: Lei Sun / Xinzheng Zhang / Song Gao / Prashant A Rao / Victor Padilla-Sanchez / Zhenguo Chen / Siyang Sun / Ye Xiang / Sriram Subramaniam / Venigalla B Rao / Michael G Rossmann /
Abstract: The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage ...The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id / _em_software.name
Revision 1.2Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
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] / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Portal protein gp20
B: Portal protein gp20
C: Portal protein gp20
D: Portal protein gp20
E: Portal protein gp20
F: Portal protein gp20
G: Portal protein gp20
H: Portal protein gp20
I: Portal protein gp20
J: Portal protein gp20
K: Portal protein gp20
L: Portal protein gp20


Theoretical massNumber of molelcules
Total (without water)640,30112
Polymers640,30112
Non-polymers00
Water0
1


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

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Components

#1: Protein
Portal protein gp20 / Gene product 20 / gp20


Mass: 53358.414 Da / Num. of mol.: 12 / Fragment: UNP residues 74-524
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 20 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P13334

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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: T4 portal protein gp20 / Type: VIRUS / Details: dodecamer
Molecular weightValue: 0.66 MDa / Experimental value: YES
Buffer solutionName: 20 mM Tris-HCl, 400 mM NaCl, 5 mM EDTA / pH: 7.8 / Details: 20 mM Tris-HCl, 400 mM NaCl, 5 mM EDTA
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R1.2/1.3 holey carbon on 200 mesh copper
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 120 K / Humidity: 90 %
Details: Blot for 7 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
Method: Blot for 7 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 10, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Calibrated magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen holder type: Liquid nitrogen-cooled / Temperature: 100 K / Temperature (max): 105 K / Temperature (min): 80 K
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
EM imaging opticsEnergyfilter name: GIF / Energyfilter upper: 25 eV / Energyfilter lower: 0 eV
Image scansNum. digital images: 839
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionMethod: Cross-common lines / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98000 / Nominal pixel size: 1 Å / Actual pixel size: 1 Å
Details: FSC was calculated from two independent reconstructions. Particles were selected using an automatic selection program. (Single particle--Applied symmetry: C12)
Num. of class averages: 15 / Symmetry type: POINT
RefinementResolution: 3.6→3.6 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 2016 0.23 %
Rwork0.2644 878498 -
obs0.2644 880514 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 302.6 Å2 / Biso mean: 83.0196 Å2 / Biso min: 6.59 Å2
Refinement stepCycle: LAST / Resolution: 3.63→272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41280 0 0 0 41280
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00942060
ELECTRON MICROSCOPYf_angle_d1.39156784
ELECTRON MICROSCOPYf_chiral_restr0.066240
ELECTRON MICROSCOPYf_plane_restr0.0067404
ELECTRON MICROSCOPYf_dihedral_angle_d15.88215876
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6302-3.7210.36331440.42776292063064100
3.721-3.82160.32581680.36296322363391100
3.8216-3.93410.27091200.31386239062510100
3.9341-4.06110.34651560.30536296063116100
4.0611-4.20620.34591440.28596246862612100
4.2062-4.37470.26281440.26426313463278100
4.3747-4.57380.26911440.25556264762791100
4.5738-4.81490.21571320.226257262704100
4.8149-5.11660.17591320.22286302863160100
5.1166-5.51170.24681440.24246248462628100
5.5117-6.06640.37871440.28256267162815100
6.0664-6.94430.22331800.2836287163051100
6.9443-8.74920.35691080.25866285562963100
8.7492-272.76660.22051560.1833622756243199

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