[English] 日本語
Yorodumi
- PDB-1t6o: Nucleocapsid-binding domain of the measles virus P protein (amino... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t6o
TitleNucleocapsid-binding domain of the measles virus P protein (amino acids 457-507) in complex with amino acids 486-505 of the measles virus N protein
Components
  • (phosphoprotein) x 2
  • linker
KeywordsVIRAL PROTEIN / four helix bundle
Function / homology
Function and homology information


helical viral capsid / viral genome replication / viral nucleocapsid / host cell cytoplasm / molecular adaptor activity / ribonucleoprotein complex / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / RNA binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Phosphoprotein / Nucleoprotein
Similarity search - Component
Biological speciesMeasles virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKingston, R.L. / Hamel, D.J. / Gay, L.S. / Dahlquist, F.W. / Matthews, B.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis for the attachment of a paramyxoviral polymerase to its template.
Authors: Kingston, R.L. / Hamel, D.J. / Gay, L.S. / Dahlquist, F.W. / Matthews, B.W.
#1: Journal: To be Published
Title: Characterization of nucleocapsid binding by the measles and the mumps virus phosphoprotein
Authors: Kingston, R.L. / Baase, W.A. / Gay, L.S.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Structure of a chimeric molecule encompassing amino acids 457-507 of measles P and 486-505 ...SEQUENCE Structure of a chimeric molecule encompassing amino acids 457-507 of measles P and 486-505 of measles N. They are connected by a flexible 8 amino acid linker (GS)4, which is largely disordered in the crystal structure. The asymmetric unit of the crystal contains the P moiety from one molecule (chain A) bound to the N moiety of a different molecule (Chain B). Link record between chain A and L is not provided since the part of the chain L which is linked to chain A is missing from the coordinates due to lack of electron density.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: phosphoprotein
L: linker
B: phosphoprotein


Theoretical massNumber of molelcules
Total (without water)8,6483
Polymers8,6483
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.226, 42.226, 81.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein phosphoprotein /


Mass: 5891.055 Da / Num. of mol.: 1 / Fragment: residues 457-507 / Mutation: P458G
Source method: isolated from a genetically manipulated source
Details: Chimeric molecule encompassing amino acids 457-507 of measles P (chain A) and 486-505 of measles N (chain B). They are connected by a flexible 8 amino acid linker (GS)4 (chain L)
Source: (gene. exp.) Measles virus / Genus: Morbillivirus / Strain: Moraten vaccine strain / Gene: P/V / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star(DE3) / References: GenBank: 9181875, UniProt: Q77M42*PLUS
#2: Protein/peptide linker


Mass: 594.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic linker
#3: Protein/peptide phosphoprotein /


Mass: 2162.453 Da / Num. of mol.: 1 / Fragment: residues 486-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus / Genus: Morbillivirus / Strain: Moraten vaccine strain / Gene: N / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star(DE3) / References: GenBank: 9181874, UniProt: Q77M43*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 9.1
Details: 0.2M AMPSO/KOH buffer, 0.5 - 1.0 M Ammonium sulfate, pH 9.1, VAPOR DIFFUSION, temperature 296K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 4, 2004
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 5306 / Num. obs: 5306 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.03 Å / % possible all: 96.4

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKS.pdb

1oks


Resolution: 2→25 Å / Isotropic thermal model: Individual Isotropic B / Cross valid method: test set omitted from all refinement / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 307 -RANDOM
Rwork0.23 ---
all0.232 5306 --
obs0.232 5306 97.5 %-
Solvent computationSolvent model: Moews & Kretsinger / Bsol: 300 Å2 / ksol: 0.85 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.884 Å20 Å20 Å2
2---2.884 Å20 Å2
3---5.768 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 0 28 576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.004827
X-RAY DIFFRACTIONt_angle_deg0.84607
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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