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- PDB-7ook: Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ -

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Entry
Database: PDB / ID: 7ook
TitleBacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ
ComponentsMajor capsid protein P3
KeywordsVIRAL PROTEIN / protein complex / chlorpromazine (CPZ)
Function / homologyBacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein / Group II dsDNA virus coat/capsid protein / Viral coat protein subunit / viral capsid / Chem-Z80 / Major capsid protein P3
Function and homology information
Biological speciesEnterobacteria phage PRD1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsDuyvesteyn, H.M.E. / Peccati, F. / Martinez-Castillo, A. / Jimenez-Oses, G. / Oksanen, H.M. / Stuart, D.I. / Abrescia, N.G.A.
Funding support Spain, United Kingdom, 5items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)RTI2018-095700-B-I00 Spain
Ministry of Economy and Competitiveness (MINECO)RTI2018-099592-B-C22 Spain
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome TrustALR00750 United Kingdom
Ministry of Economy and Competitiveness (MINECO)SEV-2016-0644 Spain
Citation
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2002
Title: The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution.
Authors: Stacy D Benson / Jaana K H Bamford / Dennis H Bamford / Roger M Burnett /
Abstract: P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now ...P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now been extended to 1.65 A resolution (R(work) = 19.0% and R(free) = 20.8%). The new high-resolution model shows that P3 forms crystals through hydrophobic patches solvated by 2-methyl-2,4-pentanediol molecules. It reveals details of how the molecule's high stability may be achieved through ordered solvent in addition to intra- and intersubunit interactions. Of particular importance is a 'puddle' at the top of the molecule containing a four-layer deep hydration shell that cross-links a complex structural feature formed by 'trimerization loops'. These loops also link subunits by extending over a neighbor to reach the third subunit in the trimer. As each subunit has two eight-stranded viral jelly rolls, the trimer has a pseudo-hexagonal shape to allow close packing in its 240 hexavalent capsid positions. Flexible regions in P3 facilitate these interactions within the capsid and with the underlying membrane. A selenometh-ionine P3 derivative, with which the structure was solved, has been refined to 2.2 A resolution (R(work) = 20.1% and R(free) = 22.8%). The derivatized molecule is essentially unchanged, although synchrotron radiation has the curious effect of causing it to rotate about its threefold axis. P3 is a second example of a trimeric 'double-barrel' protein that forms a stable building block with optimal shape for constructing a large icosahedral viral capsid. A major difference is that hexon has long variable loops that distinguish different adenovirus species. The short loops in P3 and the severe constraints of its various interactions explain why the PRD1 family has highly conserved coat proteins.
#2: Journal: Cell / Year: 1999
Title: Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures.
Authors: S D Benson / J K Bamford / D H Bamford / R M Burnett /
Abstract: The unusual bacteriophage PRD1 features a membrane beneath its icosahedral protein coat. The crystal structure of the major coat protein, P3, at 1.85 A resolution reveals a molecule with three ...The unusual bacteriophage PRD1 features a membrane beneath its icosahedral protein coat. The crystal structure of the major coat protein, P3, at 1.85 A resolution reveals a molecule with three interlocking subunits, each with two eight-stranded viral jelly rolls normal to the viral capsid, and putative membrane-interacting regions. Surprisingly, the P3 molecule closely resembles hexon, the equivalent protein in human adenovirus. Both viruses also have similar overall architecture, with identical capsid lattices and attachment proteins at their vertices. Although these two dsDNA viruses infect hosts from very different kingdoms, their striking similarities, from major coat protein through capsid architecture, strongly suggest their evolutionary relationship.
#3: Journal: Nature / Year: 2004
Title: Insights into assembly from structural analysis of bacteriophage PRD1.
Authors: Nicola G A Abrescia / Joseph J B Cockburn / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / Sarah J Butcher / Stephen D Fuller / Carmen San Martín / Roger M Burnett / David I ...Authors: Nicola G A Abrescia / Joseph J B Cockburn / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / Sarah J Butcher / Stephen D Fuller / Carmen San Martín / Roger M Burnett / David I Stuart / Dennis H Bamford / Jaana K H Bamford /
Abstract: The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 ...The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 and P31. Different structural proteins seem to have specialist roles in controlling virus assembly. The linearly extended P30 appears to nucleate the formation of the icosahedral facets (composed of trimers of the major capsid protein, P3) and acts as a molecular tape-measure, defining the size of the virus and cementing the facets together. Pentamers of P31 form the vertex base, interlocking with subunits of P3 and interacting with the membrane protein P16. The architectural similarities with adenovirus and one of the largest known virus particles PBCV-1 support the notion that the mechanism of assembly of PRD1 is scaleable and applies across the major viral lineage formed by these viruses.
#4: Journal: Nature / Year: 2004
Title: Membrane structure and interactions with protein and DNA in bacteriophage PRD1.
Authors: Joseph J B Cockburn / Nicola G A Abrescia / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / James M Benevides / George J Thomas / Jaana K H Bamford / Dennis H Bamford / David I Stuart /
Abstract: Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated ...Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated proteins present considerable difficulties for structural analysis. Although enveloped viruses have been imaged at about 9 A resolution by cryo-electron microscopy and image reconstruction, no detailed crystallographic structure of a membrane system has been described. The structure of the bacteriophage PRD1 particle, determined by X-ray crystallography at about 4 A resolution, allows the first detailed analysis of a membrane-containing virus. The architecture of the viral capsid and its implications for virus assembly are presented in the accompanying paper. Here we show that the electron density also reveals the icosahedral lipid bilayer, beneath the protein capsid, enveloping the viral DNA. The viral membrane contains about 26,000 lipid molecules asymmetrically distributed between the membrane leaflets. The inner leaflet is composed predominantly of zwitterionic phosphatidylethanolamine molecules, facilitating a very close interaction with the viral DNA, which we estimate to be packaged to a pressure of about 45 atm, factors that are likely to be important during membrane-mediated DNA translocation into the host cell. In contrast, the outer leaflet is enriched in phosphatidylglycerol and cardiolipin, which show a marked lateral segregation within the icosahedral asymmetric unit. In addition, the lipid headgroups show a surprising degree of order.
History
DepositionMay 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 7, 2022Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.country / _citation.journal_id_ISSN
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Major capsid protein P3
B: Major capsid protein P3
A: Major capsid protein P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,79224
Polymers130,4323
Non-polymers2,36021
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.750, 122.750, 126.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 3 molecules CBA

#1: Protein Major capsid protein P3 / Protein P3


Mass: 43477.414 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage PRD1 (virus) / References: UniProt: P22535

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Non-polymers , 5 types, 435 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Na
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-Z80 / 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine / Chlorpromazine / Chlorpromazine


Mass: 318.864 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C17H19ClN2S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antipsychotic*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: please see: PMID: 10499799

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.02→54.5 Å / Num. obs: 120623 / % possible obs: 99.97 % / Redundancy: 13.1 % / Biso Wilson estimate: 42.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.03
Reflection shellResolution: 2.02→2.092 Å / Redundancy: 13.3 % / Num. unique obs: 11888 / CC1/2: 0.595 / CC star: 0.864 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hx6

1hx6


Resolution: 2.23→39.83 Å / SU ML: 0.2694 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.4506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 4400 4.95 %
Rwork0.1757 84437 -
obs0.1776 88837 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.23 Å2
Refinement stepCycle: LAST / Resolution: 2.23→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8661 0 151 414 9226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00279088
X-RAY DIFFRACTIONf_angle_d0.571712449
X-RAY DIFFRACTIONf_chiral_restr0.0461398
X-RAY DIFFRACTIONf_plane_restr0.00421629
X-RAY DIFFRACTIONf_dihedral_angle_d12.90843258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.260.32131420.27632736X-RAY DIFFRACTION99.21
2.26-2.280.29781280.27052791X-RAY DIFFRACTION99.86
2.28-2.310.30611610.26172736X-RAY DIFFRACTION99.86
2.31-2.340.30471520.26072820X-RAY DIFFRACTION100
2.34-2.370.29331600.25482736X-RAY DIFFRACTION99.97
2.37-2.40.27091460.22772821X-RAY DIFFRACTION100
2.4-2.440.25651380.21382787X-RAY DIFFRACTION99.97
2.44-2.470.24751310.21362774X-RAY DIFFRACTION100
2.47-2.510.24311360.21042816X-RAY DIFFRACTION100
2.51-2.550.25141490.20362793X-RAY DIFFRACTION100
2.55-2.60.24521480.19862796X-RAY DIFFRACTION99.93
2.6-2.640.22421640.19372784X-RAY DIFFRACTION100
2.64-2.690.26561420.20132783X-RAY DIFFRACTION100
2.69-2.750.26891490.20712808X-RAY DIFFRACTION100
2.75-2.810.24621460.21162788X-RAY DIFFRACTION100
2.81-2.870.25241760.19552767X-RAY DIFFRACTION99.97
2.87-2.950.22211680.17962777X-RAY DIFFRACTION99.97
2.95-3.030.22731590.172805X-RAY DIFFRACTION99.97
3.03-3.120.19591640.17282773X-RAY DIFFRACTION99.93
3.12-3.220.24821340.16972821X-RAY DIFFRACTION99.97
3.22-3.330.18381450.16582842X-RAY DIFFRACTION99.93
3.33-3.460.19091400.172814X-RAY DIFFRACTION99.9
3.46-3.620.21561480.1632816X-RAY DIFFRACTION99.97
3.62-3.810.20881130.16352860X-RAY DIFFRACTION99.93
3.81-4.050.17931140.14192880X-RAY DIFFRACTION99.97
4.05-4.360.16171360.13932866X-RAY DIFFRACTION99.93
4.36-4.80.17441850.12932812X-RAY DIFFRACTION100
4.8-5.50.18141380.1422882X-RAY DIFFRACTION100
5.5-6.920.19971660.192896X-RAY DIFFRACTION99.97
6.92-39.830.26031220.19763057X-RAY DIFFRACTION99.5

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