[English] 日本語
Yorodumi
- PDB-8b8b: Multimerization domain of Munia virus 1 phosphoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b8b
TitleMultimerization domain of Munia virus 1 phosphoprotein
ComponentsMunia Bornavirus 1 phosphoprotein
KeywordsVIRAL PROTEIN / phosphoprotein / RNA polymerase cofactor
Function / homologyNITRATE ION
Function and homology information
Biological speciesMunia Bornavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsChenavier, F. / Tarbouriech, N. / Bourhis, J.M. / Tomonaga, K. / Horie, M. / Crepin, T.
Funding support France, Japan, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE15-0026 France
Japan Society for the Promotion of Science (JSPS)JP21H01199 Japan
CitationJournal: Viruses / Year: 2022
Title: Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing.
Authors: Tarbouriech, N. / Chenavier, F. / Kawasaki, J. / Bachiri, K. / Bourhis, J.M. / Legrand, P. / Freslon, L.L. / Laurent, E.M.N. / Suberbielle, E. / Ruigrok, R.W.H. / Tomonaga, K. / Gonzalez- ...Authors: Tarbouriech, N. / Chenavier, F. / Kawasaki, J. / Bachiri, K. / Bourhis, J.M. / Legrand, P. / Freslon, L.L. / Laurent, E.M.N. / Suberbielle, E. / Ruigrok, R.W.H. / Tomonaga, K. / Gonzalez-Dunia, D. / Horie, M. / Coyaud, E. / Crepin, T.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Munia Bornavirus 1 phosphoprotein
B: Munia Bornavirus 1 phosphoprotein
C: Munia Bornavirus 1 phosphoprotein
D: Munia Bornavirus 1 phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4936
Polymers49,3694
Non-polymers1242
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, assayed by SEC-SAXS, MALLS and gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16510 Å2
ΔGint-209 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.226, 42.746, 72.195
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Munia Bornavirus 1 phosphoprotein


Mass: 12342.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Munia Bornavirus 1 / Plasmid: petM11 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): RIL
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15-18 % PEG 3350, 150 mM Mg(NO3)2, 10 mM phenol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.15→49.34 Å / Num. obs: 23663 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.037 / Net I/σ(I): 15.2
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / Num. unique obs: 2043 / CC1/2: 0.808 / Rpim(I) all: 0.471 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292125760

Resolution: 2.15→49.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.697 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3159 1083 4.6 %RANDOM
Rwork0.2195 ---
obs0.2238 22567 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.76 Å2 / Biso mean: 54.702 Å2 / Biso min: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0.04 Å2
2---0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.15→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 8 109 3059
Biso mean--58.97 57.77 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132961
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172884
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6353951
X-RAY DIFFRACTIONr_angle_other_deg1.41.5786725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47326.24125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71615637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.567159
X-RAY DIFFRACTIONr_chiral_restr0.0670.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 68 -
Rwork0.325 1644 -
all-1712 -
obs--100 %

+
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