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- PDB-4k7h: Major capsid protein P1 of the Pseudomonas phage phi6 -

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Basic information

Entry
Database: PDB / ID: 4k7h
TitleMajor capsid protein P1 of the Pseudomonas phage phi6
ComponentsMajor inner protein P1
KeywordsVIRAL PROTEIN / major capsid protein
Function / homology: / Major inner capsid protein P1 / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1
Function and homology information
Biological speciesPseudomonas phage phi6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5964 Å
AuthorsBoura, E. / Nemecek, D. / Plevka, P. / Steven, C.A. / Hurley, J.H.
CitationJournal: Structure / Year: 2013
Title: Subunit folds and maturation pathway of a dsRNA virus capsid.
Authors: Daniel Nemecek / Evzen Boura / Weimin Wu / Naiqian Cheng / Pavel Plevka / Jian Qiao / Leonard Mindich / J Bernard Heymann / James H Hurley / Alasdair C Steven /
Abstract: The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits ...The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits in its icosahedral capsid, and capsids as compartments for transcription and replication. ϕ6 assembles as a dodecahedral procapsid that undergoes major conformational changes as it matures into the spherical capsid. We determined the crystal structure of the capsid protein, P1, revealing a flattened trapezoid subunit with an α-helical fold. We also solved the procapsid with cryo-electron microscopy to comparable resolution. Fitting the crystal structure into the procapsid disclosed substantial conformational differences between the two P1 conformers. Maturation via two intermediate states involves remodeling on a similar scale, besides huge rigid-body rotations. The capsid structure and its stepwise maturation that is coupled to sequential packaging of three RNA segments sets the cystoviruses apart from other dsRNA viruses as a dynamic molecular machine.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major inner protein P1
B: Major inner protein P1
C: Major inner protein P1
D: Major inner protein P1
E: Major inner protein P1


Theoretical massNumber of molelcules
Total (without water)429,1775
Polymers429,1775
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Major inner protein P1


Theoretical massNumber of molelcules
Total (without water)85,8351
Polymers85,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Major inner protein P1


Theoretical massNumber of molelcules
Total (without water)85,8351
Polymers85,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Major inner protein P1


Theoretical massNumber of molelcules
Total (without water)85,8351
Polymers85,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Major inner protein P1


Theoretical massNumber of molelcules
Total (without water)85,8351
Polymers85,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Major inner protein P1


Theoretical massNumber of molelcules
Total (without water)85,8351
Polymers85,8351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)182.591, 278.852, 246.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Major inner protein P1


Mass: 85835.453 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phi6 (virus) / Gene: P1 / Plasmid: pRSFD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11126

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 HEPES, pH 7.5, 180 mM calcium acetate, 10 mM EDTA, 39% PEG 400, 1:1 molar mixture with P7 protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97899 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 3.596→42 Å / Num. all: 73087 / Num. obs: 66561 / % possible obs: 91.07 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.7 % / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Net I/σ(I): 11.15
Reflection shellResolution: 3.596→3.66 Å / Mean I/σ(I) obs: 2.04 / % possible all: 41.67

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: cryoEM map

Resolution: 3.5964→40.92 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 3349 5.03 %RANDOM
Rwork0.2168 ---
obs0.2196 66532 91.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5964→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29340 0 0 0 29340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829940
X-RAY DIFFRACTIONf_angle_d1.41140730
X-RAY DIFFRACTIONf_dihedral_angle_d15.410790
X-RAY DIFFRACTIONf_chiral_restr0.0944685
X-RAY DIFFRACTIONf_plane_restr0.0075280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5964-3.64780.3604570.32981020X-RAY DIFFRACTION35
3.6478-3.70220.3895600.31641264X-RAY DIFFRACTION44
3.7022-3.760.3574890.31361695X-RAY DIFFRACTION60
3.76-3.82160.35011110.31422173X-RAY DIFFRACTION76
3.8216-3.88750.32991170.28482387X-RAY DIFFRACTION83
3.8875-3.95810.35911410.2772602X-RAY DIFFRACTION91
3.9581-4.03420.33841640.27962743X-RAY DIFFRACTION96
4.0342-4.11640.33261500.26642837X-RAY DIFFRACTION99
4.1164-4.20590.30941500.25872856X-RAY DIFFRACTION100
4.2059-4.30360.33381410.23852884X-RAY DIFFRACTION100
4.3036-4.41110.28991550.21852869X-RAY DIFFRACTION100
4.4111-4.53020.29321530.2172881X-RAY DIFFRACTION100
4.5302-4.66330.26621760.21072863X-RAY DIFFRACTION100
4.6633-4.81360.23121430.19712874X-RAY DIFFRACTION100
4.8136-4.98540.27131570.20342866X-RAY DIFFRACTION100
4.9854-5.18460.27911690.21242884X-RAY DIFFRACTION100
5.1846-5.42010.28551460.21632896X-RAY DIFFRACTION100
5.4201-5.70510.31071540.2182899X-RAY DIFFRACTION100
5.7051-6.06150.29281730.21232890X-RAY DIFFRACTION100
6.0615-6.52780.25541280.21252928X-RAY DIFFRACTION100
6.5278-7.18150.28371560.21172913X-RAY DIFFRACTION100
7.1815-8.21340.22391460.19442937X-RAY DIFFRACTION100
8.2134-10.32050.2131520.15662971X-RAY DIFFRACTION100
10.3205-40.92310.23031610.20873051X-RAY DIFFRACTION100

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