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- PDB-6ty2: CT PART CRYSTAL STRUCTURE OF THE RYMV-ENCODED VIRAL RNA SILENCING... -

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Basic information

Entry
Database: PDB / ID: 6ty2
TitleCT PART CRYSTAL STRUCTURE OF THE RYMV-ENCODED VIRAL RNA SILENCING SUPPRESSOR P1
Componentsp1
KeywordsRNA BINDING PROTEIN / ZINC FINGERS / RNA SILENCING SUPPRESSOR
Function / homologymetal ion binding / p1
Function and homology information
Biological speciesRice yellow mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsVignols, F. / Hoh, F.
Citation
Journal: J.Mol.Biol. / Year: 2022
Title: A Flexible and Original Architecture of Two Unrelated Zinc Fingers Underlies the Role of the Multitask P1 in RYMV Spread.
Authors: Poignavent, V. / Hoh, F. / Terral, G. / Yang, Y. / Gillet, F.X. / Kim, J.H. / Allemand, F. / Lacombe, E. / Brugidou, C. / Cianferani, S. / Demene, H. / Vignols, F.
#1: Journal: J. Mol. Biol. / Year: 2013
Title: The RYMV-encoded viral suppressor of RNA silencing P1 is a zinc-binding protein with redox-dependent flexibility.
Authors: Gillet, F.X. / Cattoni, D.I. / Petiot-Becard, S. / Delalande, F. / Poignavent, V. / Brizard, J.P. / Bessin, Y. / Dorsselaer, A.V. / Declerck, N. / Sanglier-Cianferani, S. / Brugidou, C. / Vignols, F.
#2: Journal: Biomol NMR Assign / Year: 2019
Title: NMR chemical shift backbone assignment of the viral protein P1 encoded by the African Rice Yellow Mottle Virus.
Authors: Yang, Y. / Poignavent, V. / Gillet, F.X. / Vignols, F. / Demene, H.
History
DepositionJan 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p1
B: p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0014
Polymers12,8702
Non-polymers1312
Water86548
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-2 kcal/mol
Surface area7620 Å2
Unit cell
Length a, b, c (Å)38.081, 31.188, 41.980
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein p1


Mass: 6435.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rice yellow mottle virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q709H6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tri-Sodium citrate pH 5.6, 20 %(v/v) Isopropanol and 20 %(w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.253 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.253 Å / Relative weight: 1
ReflectionResolution: 1.68→41.29 Å / Num. obs: 11192 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 1 / CC star: 0.08 / Rmerge(I) obs: 0.01 / Rrim(I) all: 0.015 / Net I/σ(I): 7
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1535 / Rpim(I) all: 0.6 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALA3.3.21data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→37.368 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.26
RfactorNum. reflection% reflection
Rfree0.2267 344 5.03 %
Rwork0.1935 --
obs0.1953 6835 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→37.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 0 2 48 897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007859
X-RAY DIFFRACTIONf_angle_d1.0691154
X-RAY DIFFRACTIONf_dihedral_angle_d13.4332
X-RAY DIFFRACTIONf_chiral_restr0.041120
X-RAY DIFFRACTIONf_plane_restr0.004159
LS refinement shellResolution: 1.9805→2.4951 Å
RfactorNum. reflection% reflection
Rfree0.2782 167 -
Rwork0.2148 3225 -
obs--99 %

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