[English] 日本語
Yorodumi
- PDB-5y6j: Structure of Tomato spotted wilt virus nucleocapsid protein with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y6j
TitleStructure of Tomato spotted wilt virus nucleocapsid protein with alternative oligomerization state
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / TSWV / nucleocapsid protein / NP / oligomerization
Function / homologyTospovirus nucleocapsid protein / Tospovirus nucleocapsid protein / viral nucleocapsid / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesTomato spotted wilt virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.811 Å
AuthorsGuo, Y. / Dong, S. / Lou, Z.
CitationJournal: J. Virol. / Year: 2017
Title: Distinct Mechanism for the Formation of the Ribonucleoprotein Complex of Tomato Spotted Wilt Virus.
Authors: Guo, Y. / Liu, B. / Ding, Z. / Li, G. / Liu, M. / Zhu, D. / Sun, Y. / Dong, S. / Lou, Z.
History
DepositionAug 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)86,5253
Polymers86,5253
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-88 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.364, 76.514, 98.440
Angle α, β, γ (deg.)90.00, 93.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 28841.566 Da / Num. of mol.: 3 / Mutation: R94A, R95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato spotted wilt virus / Production host: Escherichia coli (E. coli) / References: UniProt: H6UMW9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M BIS-TRIS pH 7.0; 22% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH); 20% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20050 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 21.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.811→49.492 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 1006 5.08 %
Rwork0.2315 --
obs0.2338 19806 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.811→49.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5739 0 0 23 5762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035804
X-RAY DIFFRACTIONf_angle_d0.7327780
X-RAY DIFFRACTIONf_dihedral_angle_d4.6163611
X-RAY DIFFRACTIONf_chiral_restr0.039922
X-RAY DIFFRACTIONf_plane_restr0.004968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8114-2.95960.35691260.30912434X-RAY DIFFRACTION90
2.9596-3.1450.34151240.28262718X-RAY DIFFRACTION100
3.145-3.38780.30991370.26552718X-RAY DIFFRACTION100
3.3878-3.72870.31381690.24942694X-RAY DIFFRACTION100
3.7287-4.26790.26871530.20942725X-RAY DIFFRACTION100
4.2679-5.37610.22441380.20332737X-RAY DIFFRACTION100
5.3761-49.49920.23741590.2022774X-RAY DIFFRACTION99

+
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