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- PDB-1hb5: quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obt... -

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Entry
Database: PDB / ID: 1hb5
Titlequasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography.
ComponentsBACTERIOPHAGE PRD1 P3-SHELL
KeywordsVIRUS / VIRUS/VIRAL PROTEIN / TECTIVIRIDAE / BACTERIOPHAGE PRD1 / CRYO- EM / IMAGE RECONSTRUCTION / ICOSAHEDRAL VIRUS
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 / Major capsid protein P3
Function and homology information
Biological speciesBACTERIOPHAGE PRD1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsSan Martin, C. / Burnett, R.M. / De Haas, F. / Heinkel, R. / Rutten, T. / Fuller, S.D. / Butcher, S.J. / Bamford, D.H.
Citation
Journal: Structure / Year: 2001
Title: Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions.
Authors: C S Martín / R M Burnett / F de Haas / R Heinkel / T Rutten / S D Fuller / S J Butcher / D H Bamford /
Abstract: BACKGROUND: The dsDNA bacteriophage PRD1 has a membrane inside its icosahedral capsid. While its large size (66 MDa) hinders the study of the complete virion at atomic resolution, a 1.65-A ...BACKGROUND: The dsDNA bacteriophage PRD1 has a membrane inside its icosahedral capsid. While its large size (66 MDa) hinders the study of the complete virion at atomic resolution, a 1.65-A crystallographic structure of its major coat protein, P3, is available. Cryo-electron microscopy (cryo-EM) and three-dimensional reconstruction have shown the capsid at 20-28 A resolution. Striking architectural similarities between PRD1 and the mammalian adenovirus indicate a common ancestor.
RESULTS: The P3 atomic structure has been fitted into improved cryo-EM reconstructions for three types of PRD1 particles: the wild-type virion, a packaging mutant without DNA, and a P3-shell lacking ...RESULTS: The P3 atomic structure has been fitted into improved cryo-EM reconstructions for three types of PRD1 particles: the wild-type virion, a packaging mutant without DNA, and a P3-shell lacking the membrane and the vertices. Establishing the absolute EM scale was crucial for an accurate match. The resulting "quasi-atomic" models of the capsid define the residues involved in the major P3 interactions, within the quasi-equivalent interfaces and with the membrane, and show how these are altered upon DNA packaging.
CONCLUSIONS: The new cryo-EM reconstructions reveal the structure of the PRD1 vertex and the concentric packing of DNA. The capsid is essentially unchanged upon DNA packaging, with alterations ...CONCLUSIONS: The new cryo-EM reconstructions reveal the structure of the PRD1 vertex and the concentric packing of DNA. The capsid is essentially unchanged upon DNA packaging, with alterations limited to those P3 residues involved in membrane contacts. These are restricted to a few of the N termini along the icosahedral edges in the empty particle; DNA packaging leads to a 4-fold increase in the number of contacts, including almost all copies of the N terminus and the loop between the two beta barrels. Analysis of the P3 residues in each quasi-equivalent interface suggests two sites for minor proteins in the capsid edges, analogous to those in adenovirus.
#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.
History
DepositionApr 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Other / Version format compliance
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4Jan 31, 2018Group: Data processing / Category: em_software / Item: _em_software.details / _em_software.name
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: BACTERIOPHAGE PRD1 P3-SHELL
B: BACTERIOPHAGE PRD1 P3-SHELL
C: BACTERIOPHAGE PRD1 P3-SHELL
D: BACTERIOPHAGE PRD1 P3-SHELL
E: BACTERIOPHAGE PRD1 P3-SHELL
F: BACTERIOPHAGE PRD1 P3-SHELL
G: BACTERIOPHAGE PRD1 P3-SHELL
H: BACTERIOPHAGE PRD1 P3-SHELL
I: BACTERIOPHAGE PRD1 P3-SHELL


Theoretical massNumber of molelcules
Total (without water)390,1169
Polymers390,1169
Non-polymers00
Water00
1
A: BACTERIOPHAGE PRD1 P3-SHELL
B: BACTERIOPHAGE PRD1 P3-SHELL
C: BACTERIOPHAGE PRD1 P3-SHELL
D: BACTERIOPHAGE PRD1 P3-SHELL
E: BACTERIOPHAGE PRD1 P3-SHELL
F: BACTERIOPHAGE PRD1 P3-SHELL
G: BACTERIOPHAGE PRD1 P3-SHELL
H: BACTERIOPHAGE PRD1 P3-SHELL
I: BACTERIOPHAGE PRD1 P3-SHELL
x 60


Theoretical massNumber of molelcules
Total (without water)23,406,958540
Polymers23,406,958540
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BACTERIOPHAGE PRD1 P3-SHELL
B: BACTERIOPHAGE PRD1 P3-SHELL
C: BACTERIOPHAGE PRD1 P3-SHELL
D: BACTERIOPHAGE PRD1 P3-SHELL
E: BACTERIOPHAGE PRD1 P3-SHELL
F: BACTERIOPHAGE PRD1 P3-SHELL
G: BACTERIOPHAGE PRD1 P3-SHELL
H: BACTERIOPHAGE PRD1 P3-SHELL
I: BACTERIOPHAGE PRD1 P3-SHELL
x 5


  • icosahedral pentamer
  • 1.95 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,950,58045
Polymers1,950,58045
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: BACTERIOPHAGE PRD1 P3-SHELL
B: BACTERIOPHAGE PRD1 P3-SHELL
C: BACTERIOPHAGE PRD1 P3-SHELL
D: BACTERIOPHAGE PRD1 P3-SHELL
E: BACTERIOPHAGE PRD1 P3-SHELL
F: BACTERIOPHAGE PRD1 P3-SHELL
G: BACTERIOPHAGE PRD1 P3-SHELL
H: BACTERIOPHAGE PRD1 P3-SHELL
I: BACTERIOPHAGE PRD1 P3-SHELL
x 6


  • icosahedral 23 hexamer
  • 2.34 MDa, 54 polymers
Theoretical massNumber of molelcules
Total (without water)2,340,69654
Polymers2,340,69654
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
BACTERIOPHAGE PRD1 P3-SHELL


Mass: 43346.219 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE PRD1 (virus) / Strain: DS88 / Production host: SALMONELLA TYPHIMURIUM (bacteria) / Strain (production host): DS88 / References: UniProt: P22535
Compound detailsTHE P3-SHELL IS OBTAINED BY SDS TREATMENT OF A PACKAGING MUTANT SUS1, LEADING TO LOSS OF THE VIRAL ...THE P3-SHELL IS OBTAINED BY SDS TREATMENT OF A PACKAGING MUTANT SUS1, LEADING TO LOSS OF THE VIRAL MEMBRANE, THE VERTEX STRUCTURES AND THE PERIPENTONAL P3-TRIMERS (LUO, C. ET AL., VIROLOGY 194, 564-569, 1993) MAJOR CAPSID PROTEIN P3 REQUIRED FOR PRD1 MEMBRANE TRANSLOCATION FROM THE HOST PLASMA MEMBRANE TO EMPTY PARTICLE. PRD1 VIRION HAS AN ICOSAHEDRAL PROTEIN COAT, CONSISTING MAINLY OF PROTEIN P3 PLUS THE MINOR PROTEIN P5.

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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 PRD1 P3 SHELL / Type: VIRUS
Details: THE SAMPLE CONSISTS OF THE ADENOVIRUS-RELATED BACTERIOPHAGE PRD1. 400 MESH COPPER GLOW DISCHARGE SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE.
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGE VITRIFICATION

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Jun 15, 1998
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 4100 nm / Nominal defocus min: 1300 nm / Cs: 2 mm
Specimen holderTemperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 5
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2Omodel fitting
3X-PLORmodel fitting
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: ICOSAHEDRAL / Resolution: 12 Å / Num. of particles: 471 / Nominal pixel size: 3.68 Å / Actual pixel size: 3.39 Å
Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS OBTAINED USING THE X-RAY STRUCTURE OF THE P3 TRIMER AS A REFERENCE. AFTER AN INITIAL FITTING USING THE NOMINAL PIXEL SIZE, THE P3 ...Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS OBTAINED USING THE X-RAY STRUCTURE OF THE P3 TRIMER AS A REFERENCE. AFTER AN INITIAL FITTING USING THE NOMINAL PIXEL SIZE, THE P3 TRIMERS IN THE ICOSAHEDRAL ASYMMETRIC UNIT WERE GRADUALLY TRANSLATED TOWARDS THE CENTER OF THE PARTICLE UNTIL THE CRYSTALLOGRAPHIC R-FACTOR WAS MINIMISED.
Details: THE ORIENTATIONS WERE REFINED BY THE CROSS COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER TRANSFORM METHOD. MODEL-BASED, POLAR-FOURIER-TRANSFORM (FULLER ET AL. 1996, J.STRUC.BIOL. ...Details: THE ORIENTATIONS WERE REFINED BY THE CROSS COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER TRANSFORM METHOD. MODEL-BASED, POLAR-FOURIER-TRANSFORM (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130) MODEL-BASED CROSS COMMON LINES SEARCH AND REFINEMENT (CROWTHER ET AL. 1970, NATURE (LONDON) 226, 421-425; FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55; FERLENGHI ET AL. 1998, J.MOL.BIOL. 283, 71-81). THE EFFECTIVE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 25 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND CALCULATING THE FOURIER SHELL CORRELATION OBTAINED FROM SEPARATE RECONSTRUCTIONS (HARAUZ AND VAN HEEL 1986, OPTIK 73, 146-156). THE EIGENVALUE SPECTRUM GAVE AN INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 100. THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. RESIDUES NOT VISIBLE IN THE ORIGINAL CRYSTAL STRUCTURES ARE NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factor
Details: METHOD--THE CRYSTAL STRUCTURE OF THE MAJOR COAT PROTEIN P3 (PDB FILE 1HX6) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY ...Details: METHOD--THE CRYSTAL STRUCTURE OF THE MAJOR COAT PROTEIN P3 (PDB FILE 1HX6) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT TRIMERS IN THE ICOSAHEDRAL ASYMMETRIC UNIT. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN RECIPROCAL SPACE WITH THE PROGRAM XPLOR. QUALITY OF THE FIT R- FACTOR= 0.312, CROSS-CORRELATION COEFFICIENT 0.933, ATOMS OUTSIDE DENSITY PER ICOSAHEDRAL ASYMMETRIC UNIT 180 (0.7%), ATOM CLASHES PER ICOSAHEDRAL ASYMMETRIC UNIT 121 (0.5%) REFINEMENT PROTOCOL--RIGID BODY REFINEMENT
Atomic model buildingPDB-ID: 1HX6

1hx6


Accession code: 1HX6 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 12 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25812 0 0 0 25812

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