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- PDB-1gw8: quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant... -

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Entry
Database: PDB / ID: 1gw8
Titlequasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography.
ComponentsMAJOR CAPSID PROTEIN
KeywordsVIRUS/VIRAL PROTEIN / TECTIVIRIDAE / BACTERIOPHAGE PRD1 / CRYO- EM / IMAGE RECONSTRUCTION / ICOSAHEDRAL VIRUS / VIRUS-VIRAL PROTEIN complex
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: 13.3 Å
AuthorsSan Martin, C. / Huiskonen, J. / Bamford, J.K.H. / Butcher, S.J. / Fuller, S.D. / Bamford, D.H. / Burnett, R.M.
Citation
Journal: Nat Struct Biol / Year: 2002
Title: Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid.
Authors: Carmen San Martín / Juha T Huiskonen / Jaana K H Bamford / Sarah J Butcher / Stephen D Fuller / Dennis H Bamford / Roger M Burnett /
Abstract: Bacteriophage PRD1 shares many structural and functional similarities with adenovirus. A major difference is the PRD1 internal membrane, which acts in concert with vertex proteins to translocate the ...Bacteriophage PRD1 shares many structural and functional similarities with adenovirus. A major difference is the PRD1 internal membrane, which acts in concert with vertex proteins to translocate the phage genome into the host. Multiresolution models of the PRD1 capsid, together with genetic analyses, provide fine details of the molecular interactions associated with particle stability and membrane dynamics. The N- and C-termini of the major coat protein (P3), which are required for capsid assembly, act as conformational switches bridging capsid to membrane and linking P3 trimers. Electrostatic P3-membrane interactions increase virion stability upon DNA packaging. Newly revealed proteins suggest how the metastable vertex works and how the capsid edges are stabilized.
#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: 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.
#3: 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
DepositionMar 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2013Group: Other / Source and taxonomy
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_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Aug 21, 2019Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.6May 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
H: MAJOR CAPSID PROTEIN
I: MAJOR CAPSID PROTEIN
J: MAJOR CAPSID PROTEIN
K: MAJOR CAPSID PROTEIN
L: MAJOR CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)520,15512
Polymers520,15512
Non-polymers00
Water00
1
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
H: MAJOR CAPSID PROTEIN
I: MAJOR CAPSID PROTEIN
J: MAJOR CAPSID PROTEIN
K: MAJOR CAPSID PROTEIN
L: MAJOR CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)31,209,278720
Polymers31,209,278720
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: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
H: MAJOR CAPSID PROTEIN
I: MAJOR CAPSID PROTEIN
J: MAJOR CAPSID PROTEIN
K: MAJOR CAPSID PROTEIN
L: MAJOR CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 2.6 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,600,77360
Polymers2,600,77360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
H: MAJOR CAPSID PROTEIN
I: MAJOR CAPSID PROTEIN
J: MAJOR CAPSID PROTEIN
K: MAJOR CAPSID PROTEIN
L: MAJOR CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 3.12 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)3,120,92872
Polymers3,120,92872
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))
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
MAJOR CAPSID PROTEIN / PROTEIN P3


Mass: 43346.219 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: SUS607 MUTANT LACKS THE VIRAL MEMBRANE AGGREGATION PROTEIN P11
Source: (gene. exp.) BACTERIOPHAGE PRD1 (virus) / Plasmid: PSN3 / Production host: SALMONELLA TYPHIMURIUM (bacteria) / Strain (production host): DS88 / References: UniProt: P22535
Compound detailsBACTERIOPHAGE PRD1 SUS607 MUTANT LACKS THE VIRAL MEMBRANE AGGREGATION PROTEIN P11

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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 SUS607 / Type: VIRUS
Buffer solutionName: TRIS / pH: 7.2 / Details: TRIS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: ETHANE
Crystal grow
*PLUS
Method: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Dec 1, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 45100 X / Nominal defocus max: 4100 nm / Nominal defocus min: 1300 nm / Cs: 2 mm
Specimen holderTemperature: 95 K
Image recordingElectron dose: 6 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 21
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1EMfitmodel fitting
2MRC IMAGE PROCESSING PACKAGE3D reconstructionMRC_ICOS
3SPIDER3D reconstruction
CTF correctionDetails: PHASE RESTORATION BY CTF- MULTIPLICATION OF IMAGES; AMPLITUDE RESTORATION BY COMPARISON WITH QUASI- ATOMIC MODEL
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: POLAR FOURIER TRANSFORM, CROSS- COMMON LINES / Resolution: 13.3 Å / Num. of particles: 1729 / Nominal pixel size: 3.68 Å / Actual pixel size: 3.32 Å / Magnification calibration: COMPARISON WITH X- RAY DATA
Details: RIGID BODY REFINEMENT AGAINST CRYO-EM MAP XPLOR 3.851 (BRUNGER). DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH INFINITY RESOLUTION RANGE LOW 15A DATA CUTOFF (SIGMA(F)) 0.0 NUMBER OF ...Details: RIGID BODY REFINEMENT AGAINST CRYO-EM MAP XPLOR 3.851 (BRUNGER). DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH INFINITY RESOLUTION RANGE LOW 15A DATA CUTOFF (SIGMA(F)) 0.0 NUMBER OF REFLECTIONS 1430672 FIT TO DATA USED IN
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factor / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1HX6

1hx6


Accession code: 1HX6 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 13.3 Å
Refinement stepCycle: LAST / Highest resolution: 13.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34170 0 0 0 34170

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