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- PDB-2fz2: Structure of Turnip Yellow Mosaic Virus at 100 K -

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Basic information

Entry
Database: PDB / ID: 2fz2
TitleStructure of Turnip Yellow Mosaic Virus at 100 K
Components
  • 5'-R(*CP*CP*C)-3'
  • Coat protein
KeywordsVirus/RNA / Plant virus / Coat protein / Capsid protein / Tymoviruses / TYMV / RNA / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Tymovirus coat protein / Tymovirus coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTurnip yellow mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLarson, S.B. / Lucas, R.W. / McPherson, A.
Citation
Journal: Virology / Year: 2005
Title: The RNA of turnip yellow mosaic virus exhibits icosahedral order.
Authors: Larson, S.B. / Lucas, R.W. / Greenwood, A. / McPherson, A.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal structure of turnip yellow mosaic virus.
Authors: Canady, M.A. / Larson, S.B. / Day, J. / McPherson, A.
#2: Journal: Proteins / Year: 1995
Title: Preliminary X-ray diffraction analysis of crystals of turnip yellow mosaic virus (TYMV).
Authors: Canady, M.A. / Day, J. / McPherson, A.
#3: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of an empty capsid of turnip yellow mosaic virus.
Authors: van Roon, A.M. / Bink, H.H. / Plaisier, J.R. / Pleij, C.W. / Abrahams, J.P. / Pannu, N.S.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-R(*CP*CP*C)-3'
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)61,4924
Polymers61,4924
Non-polymers00
Water0
1
D: 5'-R(*CP*CP*C)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,689,547240
Polymers3,689,547240
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
D: 5'-R(*CP*CP*C)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 307 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)307,46220
Polymers307,46220
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
D: 5'-R(*CP*CP*C)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 369 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)368,95524
Polymers368,95524
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
D: 5'-R(*CP*CP*C)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 15


  • crystal asymmetric unit, crystal frame
  • 922 kDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)922,38760
Polymers922,38760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)511.530, 511.530, 303.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)127.8825, -206.91823, 79.03573
3generate(-0.30901699, -0.5, -0.80901699), (0.5, -0.80901699, 0.30901699), (-0.80901699, -0.30901699, 0.5)334.80073, -127.8825, 206.91823
4generate(-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5)334.80073, 127.8825, 206.91823
5generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699)127.8825, 206.91823, 79.03573
6generate(-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699)462.68323, 79.03573, 127.8825
7generate(-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)383.6475, 206.91823, -79.03573
8generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)127.8825, 206.91823, -79.03573
9generate(0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699)48.84677, 79.03573, 127.8825
10generate(-1), (1), (-1)255.765, 255.765
11generate(0.80901699, -0.30901699, -0.5), (0.30901699, -0.5, 0.80901699), (-0.5, -0.80901699, -0.30901699)48.84677, -79.03573, 127.8825
12generate(0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.30901699, -0.5)176.72927, 127.8825, 206.91823
13generate(-1), (-1), (1)255.765, 255.765
14generate(0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5)176.72927, 127.8825, -206.91823
15generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)48.84677, -79.03573, -127.8825

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Components

#1: RNA chain 5'-R(*CP*CP*C)-3'


Mass: 870.588 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Coat protein / Virion protein


Mass: 20207.285 Da / Num. of mol.: 3 / Fragment: Viral coat protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip yellow mosaic virus / Genus: Tymovirus / Strain: (Australian isolate) / Species (production host): Brassica rapa / Production host: Brassica rapa subsp. chinensis (bok-choy) / Strain (production host): subsp. chinensis / References: UniProt: P20125

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1.0-1.7 M NH4PO4, 0.1 M MES buffer, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211
SYNCHROTRONALS 5.0.221.25
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDDec 11, 1998Vertical and toroidal focusing mirror
ADSC QUANTUM 42CCDNov 20, 1999Vertical and toroidal focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.251
ReflectionResolution: 2.61→59.12 Å / Num. all: 247650 / Num. obs: 225845 / % possible obs: 35.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.49
Reflection shellResolution: 2.61→2.65 Å / Redundancy: 1 % / Mean I/σ(I) obs: -0.41 / Num. unique all: 172 / % possible all: 0.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AUY

1auy


Resolution: 2.9→59.12 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 171751.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Simulated annealing and conjugate gradient minimization. Stereochemistry target values for the nucleic acid fragment are from Parkinson, Vojtechovsky, Clowney, Brunger & Berman
RfactorNum. reflection% reflectionSelection details
Rfree0.289 10857 5 %RANDOM
Rwork0.276 ---
all0.327 246412 --
obs0.277 215839 42.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3842 Å2 / ksol: 0.394524 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å26.21 Å20 Å2
2---5.62 Å20 Å2
3---11.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.84 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 2.9→59.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 57 0 0 4122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d29.9
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it4.081.5
X-RAY DIFFRACTIONc_mcangle_it6.352
X-RAY DIFFRACTIONc_scbond_it6.882
X-RAY DIFFRACTIONc_scangle_it9.712.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.458 101 5.2 %
Rwork0.4 1857 -
obs-1958 2.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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