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- PDB-2cwo: Crystal structure of RNA silencing suppressor p21 from Beet Yello... -

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Basic information

Entry
Database: PDB / ID: 2cwo
TitleCrystal structure of RNA silencing suppressor p21 from Beet Yellows Virus
ComponentsRNA silencing suppressor
KeywordsRNA BINDING PROTEIN / Octamer / ring / head-to-head / tail-to-tail / all alpha helical / RNA-binding protein
Function / homology
Function and homology information


host cell cytoplasm / RNA binding / identical protein binding
Similarity search - Function
RNA silencing suppressor P21, C-terminal domain / RNA silencing suppressor P21, N-terminal domain / RNA silencing suppressor P21, C-terminal / Suppressor of RNA silencing P21-like, N-terminal / RNA silencing suppressor P21 C-terminal domain / Suppressor of RNA silencing P21-like N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA silencing suppressor
Similarity search - Component
Biological speciesBeet yellows virus
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.3 Å
AuthorsYe, K. / Patel, D.J.
CitationJournal: STRUCTURE / Year: 2005
Title: RNA Silencing Suppressor p21 of Beet Yellows Virus Forms an RNA Binding Octameric Ring Structure
Authors: Ye, K. / Patel, D.J.
History
DepositionJun 22, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA silencing suppressor
B: RNA silencing suppressor
C: RNA silencing suppressor
D: RNA silencing suppressor


Theoretical massNumber of molelcules
Total (without water)91,0454
Polymers91,0454
Non-polymers00
Water0
1
A: RNA silencing suppressor
B: RNA silencing suppressor
C: RNA silencing suppressor
D: RNA silencing suppressor

A: RNA silencing suppressor
B: RNA silencing suppressor
C: RNA silencing suppressor
D: RNA silencing suppressor


Theoretical massNumber of molelcules
Total (without water)182,0908
Polymers182,0908
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Unit cell
Length a, b, c (Å)199.633, 199.633, 56.122
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA1 - 9321 - 113
21METMETVALVALBB1 - 9321 - 113
31METMETVALVALCC1 - 9321 - 113
41METMETVALVALDD1 - 9321 - 113
12VALVALILEILEAA94 - 177114 - 197
22VALVALILEILEBB94 - 177114 - 197
32VALVALILEILECC94 - 177114 - 197
42VALVALILEILEDD94 - 177114 - 197

NCS ensembles :
ID
1
2
DetailsThe biological assemble is a octamer generated from the tetramer in the asymmetric unit by the operation: Y,X,2-Z

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Components

#1: Protein
RNA silencing suppressor / p21


Mass: 22761.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beet yellows virus / Genus: Closterovirus / Gene: p21 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08545

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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: 3.55 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M K/Na Tartrate, 100mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 19491 / Num. obs: 19263 / % possible obs: 98.82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.6
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / Num. unique all: 1912 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 51.103 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24443 943 4.9 %RANDOM
Rwork0.21004 ---
all0.21168 18442 --
obs0.21168 18224 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 132.327 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å2-1.4 Å20 Å2
2---2.79 Å20 Å2
3---4.19 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5388 0 0 0 5388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9737304
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51723.385260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.368151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6551552
X-RAY DIFFRACTIONr_chiral_restr0.1230.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023936
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2720.22816
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.23839
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3740.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4281.53351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76425296
X-RAY DIFFRACTIONr_scbond_it1.43932280
X-RAY DIFFRACTIONr_scangle_it2.5014.52008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A669tight positional0.060.05
12B669tight positional0.050.05
13C669tight positional0.050.05
14D669tight positional0.060.05
21A678tight positional0.070.05
22B678tight positional0.050.05
23C678tight positional0.060.05
24D678tight positional0.060.05
11A669tight thermal0.110.5
12B669tight thermal0.070.5
13C669tight thermal0.070.5
14D669tight thermal0.070.5
21A678tight thermal0.140.5
22B678tight thermal0.090.5
23C678tight thermal0.10.5
24D678tight thermal0.080.5
LS refinement shellResolution: 3.3→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 74 -
Rwork0.308 1233 -
obs--95.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
115.78524.15442.42556.73621.61915.5217-0.2571.3202-0.2471-0.35030.47540.47840.239-0.2269-0.2184-0.86950.01860.056-0.57220.0727-0.445246.006104.53822.276
216.8813.911310.21345.45424.200612.3529-0.5474-0.66271.4244-0.33760.2021.2148-0.7901-1.20430.3454-0.7395-0.04340.0011-0.2290.13680.304423.833107.29423.16
33.58511.6301-0.658214.773-12.093211.9323-0.677-0.0912-0.633-3.3799-0.6136-1.19192.88410.72941.29061.28330.59740.3283-0.10950.02330.2925-0.76941.10313.926
44.43612.7467-2.189819.903-10.151910.25970.27030.23180.50930.61720.08371.2502-0.6909-0.5749-0.354-0.26040.2646-0.1098-0.3402-0.01680.1439-11.74136.97232.77
58.5473-3.38721.64052.1729-2.054610.4605-0.1483-0.27620.06530.17720.2330.1836-0.0546-0.117-0.0846-1.03270.02370.0841-0.9608-0.0934-0.42250.984111.8350.615
67.58363.0144-0.520215.44251.5474.0321-0.13291.0991-0.3925-1.10050.0035-0.98920.02570.66940.1294-0.7781-0.16340.0620.25060.11470.103517.7183.1167.158
710.4682.1322-3.60048.7780.9938.1660.22170.0321-0.0488-0.5328-0.2128-0.53330.19840.5245-0.0088-0.8545-0.0208-0.1725-0.48750.0677-0.3157-3.59170.34814.859
811.7404-7.370910.08748.9001-8.607719.0560.84782.36050.8846-1.0285-2.1531-0.97310.69022.75091.3052-0.41850.29240.15960.1490.32980.01338.05916.97543.258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 9321 - 113
2X-RAY DIFFRACTION2BB1 - 9321 - 113
3X-RAY DIFFRACTION3CC1 - 9321 - 113
4X-RAY DIFFRACTION4DD1 - 9321 - 113
5X-RAY DIFFRACTION5AA94 - 177114 - 197
6X-RAY DIFFRACTION6BB94 - 177114 - 197
7X-RAY DIFFRACTION7CC94 - 177114 - 197
8X-RAY DIFFRACTION8DD94 - 177114 - 197

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