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- PDB-2fz1: Structure of Empty Head Turnip Yellow Mosaic Virus (ATC) at 100 K -

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Basic information

Entry
Database: PDB / ID: 2fz1
TitleStructure of Empty Head Turnip Yellow Mosaic Virus (ATC) at 100 K
ComponentsCoat protein
KeywordsVIRUS / Plant virus / Coat protein / Capsid protein / Tymoviruses / TYMV / Icosahedral virus
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

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)60,6223
Polymers60,6223
Non-polymers00
Water00
1
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,637,311180
Polymers3,637,311180
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: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 303 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)303,10915
Polymers303,10915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 364 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)363,73118
Polymers363,73118
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: Coat protein
B: Coat protein
C: Coat protein
x 15


  • crystal asymmetric unit, crystal frame
  • 909 kDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)909,32845
Polymers909,32845
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)511.360, 511.360, 304.310
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)127.84, -206.84947, 79.00947
3generate(-0.30901699, -0.5, -0.80901699), (0.5, -0.80901699, 0.30901699), (-0.80901699, -0.30901699, 0.5)334.68947, -127.84, 206.84947
4generate(-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5)334.68947, 127.84, 206.84947
5generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699)127.84, 206.84947, 79.00947
6generate(-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699)462.52947, 79.00947, 127.84
7generate(-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)383.52, 206.84947, -79.00947
8generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)127.84, 206.84947, -79.00947
9generate(0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699)48.83053, 79.00947, 127.84
10generate(-1), (1), (-1)255.68, 255.68
11generate(0.80901699, -0.30901699, -0.5), (0.30901699, -0.5, 0.80901699), (-0.5, -0.80901699, -0.30901699)48.83053, -79.00947, 127.84
12generate(0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.30901699, -0.5)176.67053, 127.84, 206.84947
13generate(-1), (-1), (1)255.68, 255.68
14generate(0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5)176.67053, 127.84, -206.84947
15generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)48.83053, -79.00947, -127.84

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Components

#1: Protein Coat protein / Virion protein


Mass: 20207.285 Da / Num. of mol.: 3
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: 1

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Sample preparation

CrystalDensity Matthews: 6.34 Å3/Da / Density % sol: 80.6 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 1998 / Details: Vertical and toroidal focusing mirror
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→49.53 Å / Num. all: 322958 / Num. obs: 281901 / % possible obs: 63.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.35 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.118 / Net I/σ(I): 4.37
Reflection shellResolution: 2.89→2.94 Å / Redundancy: 1.15 % / Mean I/σ(I) obs: 0.41 / Num. unique all: 5433 / % possible all: 21.5

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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→48.64 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 129062.31 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.315 12504 5 %RANDOM
Rwork0.309 ---
all0.366 322690 --
obs0.309 249373 49.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1234 Å2 / ksol: 0.32222 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.53 Å2-0.88 Å20 Å2
2---3.61 Å20 Å2
3---11.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a0.97 Å0.94 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 0 0 4058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d28.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it4.681.5
X-RAY DIFFRACTIONc_mcangle_it7.272
X-RAY DIFFRACTIONc_scbond_it8.282
X-RAY DIFFRACTIONc_scangle_it11.52.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 131 4.4 %
Rwork0.413 2815 -
obs-2946 3.5 %
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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