[English] 日本語
Yorodumi
- PDB-8rcq: Structural flexibility of Nucleoprotein of the Toscana virus in t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rcq
TitleStructural flexibility of Nucleoprotein of the Toscana virus in the presence of a nanobody.
Components
  • Nucleoprotein
  • VHH
KeywordsVIRAL PROTEIN / Toscana virus / Nucleoprotein / SAXS / VHH / nanobody / drugs
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesToscana virus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPapageorgiou, N. / Ferron, F. / Coutard, B. / Lichiere, J. / Baklouti, A.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-BSV8-0019 France
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05-01 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody.
Authors: Papageorgiou, N. / Baklouti, A. / Lichiere, J. / Desmyter, A. / Canard, B. / Coutard, B. / Ferron, F.
History
DepositionDec 6, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionJan 31, 2024ID: 8BPK
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: VHH


Theoretical massNumber of molelcules
Total (without water)42,6152
Polymers42,6152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.755, 54.755, 380.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 27665.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toscana virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21701
#2: Antibody VHH


Mass: 14948.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5M MES, pH 6.5, 25% w/v PEG 2000

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.8→47.46 Å / Num. obs: 6413 / % possible obs: 99.47 % / Redundancy: 10.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.21 / Net I/av σ(I): 12 / Net I/σ(I): 12
Reflection shellResolution: 3.8→3.97 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 6413 / CC1/2: 0.78

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→47.46 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.35 1071 9.87 %Random
Rwork0.3 ---
obs-6413 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 0 0 2763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032805
X-RAY DIFFRACTIONf_angle_d0.5973781
X-RAY DIFFRACTIONf_dihedral_angle_d4.022392
X-RAY DIFFRACTIONf_chiral_restr0.039427
X-RAY DIFFRACTIONf_plane_restr0.004486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.970.46651350.45441215X-RAY DIFFRACTION98
3.97-4.180.48491330.40761236X-RAY DIFFRACTION100
4.18-4.440.47181370.37281187X-RAY DIFFRACTION99
4.44-4.790.3551321224X-RAY DIFFRACTION99
4.79-5.270.48591290.39491242X-RAY DIFFRACTION100
5.27-6.030.35661430.35581231X-RAY DIFFRACTION100
6.03-7.590.3251360.30891218X-RAY DIFFRACTION100
7.59-100.27331260.21851227X-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