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- PDB-6xv2: Full structure of RYMV P1 protein, derived from crystallographic ... -

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Basic information

Entry
Database: PDB / ID: 6xv2
TitleFull structure of RYMV P1 protein, derived from crystallographic and NMR data.
Componentsp1
KeywordsVIRAL PROTEIN / putative RNA binding protein / silencing suppressor
Function / homologyp1
Function and homology information
Biological speciesRice yellow mottle virus
MethodSOLUTION NMR / simulated annealing
AuthorsPoignavent, V. / Hoh, F. / Vignols, F. / Demene, H. / Yang, Y. / Gillet, F.X.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INBS-05 France
CitationJournal: 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.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0823
Polymers17,9511
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10630 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein p1


Mass: 17951.000 Da / Num. of mol.: 1
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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
133isotropic13D CBCA(CO)NH
143isotropic13D HNCA
153isotropic13D HNCO
163isotropic13D HN(CA)CB
173isotropic13D (H)CCH-TOCSY
182anisotropic22D TROSY
191anisotropic22D HSQC IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM [U-99% 15N] RYMV P1, 100 mM None NaCl, 1 mM None DTT, 60 mM None Na2SO4, 25 mM None TRIS, 90% H2O/10% D2O15N90% H2O/10% D2O
filamentous virus2500 uM 15N RYMV P1, 7 mg/mL None Pf1 phage, 200 mM None NaCl, 25 mM None TRIS, 1 mM None DTT, 90% H2O/10% D2O15N aligned90% H2O/10% D2O
solution3200 uM [U-99% 13C; U-99% 15N] RYMV P1, 100 mM None sodium chloride, 25 mM None TRIS, 1 mM None DTT, 60 mM None Na2SO4, 95% H2O/5% D2O15N,13C95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMRYMV P1[U-99% 15N]1
100 mMNaClNone1
1 mMDTTNone1
60 mMNa2SO4None1
25 mMTRISNone1
500 uMRYMV P115N2
7 mg/mLPf1 phageNone2
200 mMNaClNone2
25 mMTRISNone2
1 mMDTTNone2
200 uMRYMV P1[U-99% 13C; U-99% 15N]3
100 mMsodium chlorideNone3
25 mMTRISNone3
1 mMDTTNone3
60 mMNa2SO4None3
Sample conditionsIonic strength: 220 mM / Ionic strength err: 10 / Label: 15N / pH: 8 / PH err: 0.01 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001Cryprobe 15N, 13C, 1H
Bruker AVANCE IIIBrukerAVANCE III7002Cryprobe 15N, 13C, 1H

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
GifaDelsucprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: rigid body
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 14

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