[English] 日本語
Yorodumi
- PDB-6ty0: NT PART CRYSTAL STRUCTURE OF THE RYMV-ENCODED VIRAL RNA SILENCING... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ty0
TitleNT 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: 2.1 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: p1
B: p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0385
Polymers22,8422
Non-polymers1963
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-30 kcal/mol
Surface area10850 Å2
Unit cell
Length a, b, c (Å)195.612, 195.612, 195.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11B-202-

ZN

21A-372-

HOH

-
Components

#1: Protein p1


Mass: 11420.765 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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: 20 mM Tris pH 8, 75 mM NaCl, 1 mM DTT and 300 mM ZnCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→112.94 Å / Num. obs: 22243 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.012 / Rrim(I) all: 0.058 / Net I/σ(I): 45
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 6 / Num. unique obs: 3160 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→112.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.886 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21417 878 4.6 %RANDOM
Rwork0.18423 ---
obs0.18564 18395 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.583 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→112.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 3 135 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191593
X-RAY DIFFRACTIONr_bond_other_d0.0010.021417
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.8972187
X-RAY DIFFRACTIONr_angle_other_deg0.78633253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51123.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69115228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.709158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4874.088770
X-RAY DIFFRACTIONr_mcbond_other3.4664.085769
X-RAY DIFFRACTIONr_mcangle_it4.8126.112959
X-RAY DIFFRACTIONr_mcangle_other4.8146.116960
X-RAY DIFFRACTIONr_scbond_it4.5994.634823
X-RAY DIFFRACTIONr_scbond_other4.5994.625821
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1086.7271228
X-RAY DIFFRACTIONr_long_range_B_refined10.07835.2081824
X-RAY DIFFRACTIONr_long_range_B_other9.8934.7591785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 54 -
Rwork0.286 1335 -
obs--99.93 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more