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- PDB-6q5u: High resolution electron cryo-microscopy structure of the bacteri... -

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Basic information

Entry
Database: PDB / ID: 6q5u
TitleHigh resolution electron cryo-microscopy structure of the bacteriophage PR772
Components
  • Infectivity Protein (P16)
  • Major Capsid Protein (P3)
  • Minor Capsid Protein (P30)
  • Penton protein
  • Spike protein
KeywordsVIRUS / Phage / Tectiviridae / Membrane / double-barrel / helix turn helix / helix with a kink / beta-propeller / heteropentamer / penton
Function / homology
Function and homology information


viral capsid / membrane
Similarity search - Function
Tectiviridae, minor capsid / Tectiviridae, minor capsid / Domain of unknown function (DUF1970) / Viral coat protein p3 / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5 C-terminal domain superfamily / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P5, spike N-terminal / Adenovirus Type 2 Hexon; domain 4 ...Tectiviridae, minor capsid / Tectiviridae, minor capsid / Domain of unknown function (DUF1970) / Viral coat protein p3 / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5 C-terminal domain superfamily / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P5, spike N-terminal / Adenovirus Type 2 Hexon; domain 4 / Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein / Group II dsDNA virus coat/capsid protein / Jelly Rolls - #20 / Distorted Sandwich / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Infectivity protein / Minor capsid protein / Major capsid protein / Spike / Penton
Similarity search - Component
Biological speciesEnterobacteria phage PR772 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsNarayana Reddy, H.K. / Svenda, M.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council628-20081109822-2010-6157, 822-2012-5260 and 828-2012-108 Sweden
Knut and Alice Wallenberg FoundationKAW-2011.081 Sweden
European Research CouncilERC-291602 Sweden
Citation
Journal: Elife / Year: 2019
Title: Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture.
Authors: Hemanth Kn Reddy / Marta Carroni / Janos Hajdu / Martin Svenda /
Abstract: Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged ...Bacteriophage PR772, a member of the family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.
#1: Journal: Biorxiv / Year: 2019
Title: Electron cryo-microscopy of Bacteriophage PR772 reveals the composition and structure of the elusive vertex complex and the capsid architecture
Authors: Narayana Reddy, H.K. / Hajdu, J. / Carroni, M. / Svenda, M.
History
DepositionDec 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Category: em_admin / em_map / pdbx_database_proc
Item: _em_admin.last_update / _em_map.contour_level / _em_map.contour_level_source
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Nov 6, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
Revision 1.4Dec 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 1.5May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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Assembly

Deposited unit
A: Major Capsid Protein (P3)
B: Major Capsid Protein (P3)
C: Major Capsid Protein (P3)
D: Major Capsid Protein (P3)
E: Major Capsid Protein (P3)
F: Major Capsid Protein (P3)
G: Major Capsid Protein (P3)
H: Major Capsid Protein (P3)
I: Major Capsid Protein (P3)
J: Major Capsid Protein (P3)
K: Major Capsid Protein (P3)
L: Major Capsid Protein (P3)
M: Minor Capsid Protein (P30)
N: Infectivity Protein (P16)
O: Spike protein
P: Spike protein
Q: Spike protein
R: Penton protein
S: Penton protein


Theoretical massNumber of molelcules
Total (without water)674,92419
Polymers674,92419
Non-polymers00
Water00
1
A: Major Capsid Protein (P3)
B: Major Capsid Protein (P3)
C: Major Capsid Protein (P3)
D: Major Capsid Protein (P3)
E: Major Capsid Protein (P3)
F: Major Capsid Protein (P3)
G: Major Capsid Protein (P3)
H: Major Capsid Protein (P3)
I: Major Capsid Protein (P3)
J: Major Capsid Protein (P3)
K: Major Capsid Protein (P3)
L: Major Capsid Protein (P3)
M: Minor Capsid Protein (P30)
N: Infectivity Protein (P16)
x 60
O: Spike protein
P: Spike protein
Q: Spike protein
R: Penton protein
S: Penton protein
x 12


Theoretical massNumber of molelcules
Total (without water)34,209,061900
Polymers34,209,061900
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation70
Buried area84240 Å2
ΔGint-318 kcal/mol
Surface area192120 Å2

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Components

#1: Protein
Major Capsid Protein (P3)


Mass: 43505.492 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage PR772 (virus) / References: UniProt: Q6EDX0
#2: Protein Minor Capsid Protein (P30)


Mass: 9275.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage PR772 (virus) / References: UniProt: Q6EDW3
#3: Protein Infectivity Protein (P16)


Mass: 12616.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage PR772 (virus) / References: UniProt: Q6EDW1
#4: Protein Spike protein


Mass: 34483.898 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage PR772 (virus) / References: UniProt: Q6EDX8
#5: Protein Penton protein


Mass: 13757.388 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage PR772 (virus) / References: UniProt: Q6EDY0

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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 PR772 / Type: COMPLEX / Details: Wild type / Entity ID: all / Source: NATURAL
Molecular weightValue: 86 MDa / Experimental value: NO
Source (natural)Organism: Enterobacteria phage PR772 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Escherichia coli / Strain: C-3000
Virus shellDiameter: 750 nm / Triangulation number (T number): 25
Buffer solutionpH: 8
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298.15 K

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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 / Nominal magnification: 130000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3200
Image scansMovie frames/image: 40 / Used frames/image: 3-40

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
7Coot0.8.9.1model fitting
19PHENIXdev-3360model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 56000
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46000 / Symmetry type: POINT
Atomic model buildingB value: 104.93 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
RefinementHighest resolution: 2.75 Å / Stereochemistry target values: CORRELATION COEFFCIENT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00642657
ELECTRON MICROSCOPYf_angle_d0.80658270
ELECTRON MICROSCOPYf_dihedral_angle_d6.08225247
ELECTRON MICROSCOPYf_chiral_restr0.0556594
ELECTRON MICROSCOPYf_plane_restr0.0077697

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