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- PDB-3es5: Crystal Structure of Partitivirus (PsV-F) -

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Basic information

Entry
Database: PDB / ID: 3es5
TitleCrystal Structure of Partitivirus (PsV-F)
ComponentsPutative capsid protein
KeywordsVIRUS / Partitivirus / RNA virus / double stranded RNA virus / dsRNA virus / T=2 / "T=2" capsid / icosahedral virus
Function / homologyZinc Finger, Delta Prime; domain 3 - #60 / Zinc Finger, Delta Prime; domain 3 / Up-down Bundle / Mainly Alpha / identical protein binding / Putative capsid protein
Function and homology information
Biological speciesPenicillium stoloniferum virus F
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.3 Å
AuthorsPan, J. / Dong, L. / Lin, L. / Ochoa, W.F. / Sinkovits, R.S. / Havens, W.M. / Nibert, M.L. / Baker, T.S. / Ghabrial, S.A. / Tao, Y.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Atomic structure reveals the unique capsid organization of a dsRNA virus.
Authors: Pan, J. / Dong, L. / Lin, L. / Ochoa, W.F. / Sinkovits, R.S. / Havens, W.M. / Nibert, M.L. / Baker, T.S. / Ghabrial, S.A. / Tao, Y.J.
#1: Journal: To be Published
Title: Determination of the atomic structure of a Partitivirus by phase extension using EM map as model
Authors: Pan, J.H. / Ghabrial, S.A. / Tao, Y.Z.J.
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative capsid protein
B: Putative capsid protein


Theoretical massNumber of molelcules
Total (without water)93,1792
Polymers93,1792
Non-polymers00
Water00
1
A: Putative capsid protein
B: Putative capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,590,710120
Polymers5,590,710120
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: Putative capsid protein
B: Putative capsid protein
x 5


  • icosahedral pentamer
  • 466 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)465,89310
Polymers465,89310
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Putative capsid protein
B: Putative capsid protein
x 6


  • icosahedral 23 hexamer
  • 559 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)559,07112
Polymers559,07112
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
6
A: Putative capsid protein
B: Putative capsid protein
x 5


  • crystal asymmetric unit, crystal frame
  • 466 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)465,89310
Polymers465,89310
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)459.266, 459.266, 459.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.309017, -0.80901699, 0.5), (0.80901699, 0.5, 0.309017), (-0.5, 0.309017, 0.80901699)
3generate(-0.80901699, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.30901699, 0.809017, 0.5)
4generate(-0.809017, 0.5, -0.309017), (-0.5, -0.30901699, 0.809017), (0.309017, 0.80901699, 0.5)
5generate(0.30901699, 0.809017, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.809017)

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Components

#1: Protein Putative capsid protein


Mass: 46589.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Virus particles were produced in Penicillium stoloniferum ATCC 14586 (the strain name was not for the virus)
Source: (natural) Penicillium stoloniferum virus F / Strain: ATCC 14586 (for the host of PsV-F) / References: UniProt: Q4G3H1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 100

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Sample preparation

Crystal
ID
1
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2831vapor diffusion, hanging drop8.50.10 M Tris, 1.98 M Ammonium Sulfate, 0.10 M Potassium Fluoride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
2832vapor diffusion, hanging drop8.50.10 M Tris, 1.98 M Ammonium Sulfate, 0.10 M Sodium Tiocyanate , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
2833vapor diffusion, hanging drop8.50.10 M Tris, 1.98 M Ammonium Sulfate, 0.10 M Sodium Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12741
22741
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.9179
SYNCHROTRONCHESS F120.9179
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJan 1, 200724-inch Rh coated Si Monochromatic Mirrors (please check http://www.chess.cornell.edu/chess/east/F1.htm for details)
ADSC QUANTUM 42CCDNov 16, 200724-inch Rh coated Si Monochromatic Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Horizontal bent Si(111), asymmetrically cut with water cooled Cu BlockSINGLE WAVELENGTHMx-ray1
2Horizontal bent Si(111), asymmetrically cut with water cooled Cu BlockSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91791
21
ReflectionResolution: 3.3→50 Å / Num. obs: 119427 / % possible obs: 75.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.206 / Net I/σ(I): 4.08
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.61 / Num. unique all: 8783 / % possible all: 74.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
RAVEmodel building
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RAVEphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: cryo-EM reconstruction (resolution: 7.8 A, start resolution: 10.0 A)

Resolution: 3.3→48.96 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5407 -RANDOM
Rwork0.248 ---
all-119586 --
obs-89413 74.9 %-
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.3→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 0 0 0 5919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.356 904 -
Rwork0.332 --
obs-13571 72.9 %

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