[English] 日本語
Yorodumi
- PDB-5e4v: Crystal structure of measles N0-P complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e4v
TitleCrystal structure of measles N0-P complex
ComponentsNucleoprotein,Phosphoprotein
KeywordsVIRAL PROTEIN / paramyxovirus / nucleocapsid protein / RNA-binding protein
Function / homology
Function and homology information


host cell viral nucleoid / symbiont-mediated perturbation of host gene expression / positive regulation of viral transcription / helical viral capsid / Hsp70 protein binding / viral genome replication / molecular condensate scaffold activity / viral nucleocapsid / molecular adaptor activity / host cell cytoplasm ...host cell viral nucleoid / symbiont-mediated perturbation of host gene expression / positive regulation of viral transcription / helical viral capsid / Hsp70 protein binding / viral genome replication / molecular condensate scaffold activity / viral nucleocapsid / molecular adaptor activity / host cell cytoplasm / ribonucleoprotein complex / RNA-directed 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 / Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal
Similarity search - Domain/homology
Phosphoprotein / Nucleoprotein
Similarity search - Component
Biological speciesMeasles virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsGuryanov, S.G. / Liljeroos, L. / Kasaragod, P. / Kajander, T. / Butcher, S.J.
Funding support Finland, 6items
OrganizationGrant numberCountry
Academy of Finland139178 Finland
Academy of Finland275199 Finland
Sigrid Juselius Foundation Finland
Viikki Doctoral Programme in Molecular Biosciences Finland
Biocenter Finland Finland
Instruct National affiliate center Finland
CitationJournal: J.Virol. / Year: 2015
Title: Crystal Structure of the Measles Virus Nucleoprotein Core in Complex with an N-Terminal Region of Phosphoprotein.
Authors: Guryanov, S.G. / Liljeroos, L. / Kasaragod, P. / Kajander, T. / Butcher, S.J.
History
DepositionOct 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein,Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)48,4471
Polymers48,4471
Non-polymers00
Water1629
1
A: Nucleoprotein,Phosphoprotein

A: Nucleoprotein,Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)96,8942
Polymers96,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6520 Å2
ΔGint-73 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.140, 91.140, 94.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Nucleoprotein,Phosphoprotein / Nucleocapsid protein / Protein N


Mass: 48446.988 Da / Num. of mol.: 1
Fragment: nucleoprotein core domain with phosphoprotein binding peptide fused,nucleoprotein core domain with phosphoprotein binding peptide fused
Source method: isolated from a genetically manipulated source
Details: First residue remained from TEV cleavage site. Residues 2-389 correspond to measles nucleoprotein GenBank ID AAA18995.1 aa 21-408. Residues 390-437 correspond to measles phosphoprotein ...Details: First residue remained from TEV cleavage site. Residues 2-389 correspond to measles nucleoprotein GenBank ID AAA18995.1 aa 21-408. Residues 390-437 correspond to measles phosphoprotein GenBank ID AAF85668.1 aa 1-48 (although the full sequence of the protein in our virus strain (Halonen strain) differs by D512N variation compared to AAF85668.1, the difference does not affect the part of the sequence used in the experiment).
Source: (gene. exp.) Measles virus (strain Edmonston B), (gene. exp.) Measles virus (strain Edmonston-Moraten vaccine)
Strain: Edmonston B, Edmonston-Moraten vaccine / Gene: N, NP / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q89933, UniProt: Q77M42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: PEG 4000, sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2015 / Details: focused beam
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.71→94.07 Å / Num. obs: 12618 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 62.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.059 / Net I/σ(I): 7.5 / Num. measured all: 63741 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
2.71-2.864.90.8931.6882518170.6370.45
8.57-94.074.50.032420624600.9980.015

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia20.3.8.0data reduction
xia20.3.8.0data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CO6

4co6


Resolution: 2.71→78.93 Å / FOM work R set: 0.7854 / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 700 5.53 %Random selection
Rwork0.211 11956 --
obs0.214 12656 99.79 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.99 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 259.59 Å2 / Biso mean: 68.86 Å2 / Biso min: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.5982 Å2-0 Å2-0 Å2
2--0.5982 Å20 Å2
3----1.1965 Å2
Refinement stepCycle: final / Resolution: 2.71→78.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 0 9 2984
Biso mean---49.63 -
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053025
X-RAY DIFFRACTIONf_angle_d0.9764117
X-RAY DIFFRACTIONf_chiral_restr0.054496
X-RAY DIFFRACTIONf_plane_restr0.004526
X-RAY DIFFRACTIONf_dihedral_angle_d14.8021052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7101-2.91930.41251500.332423462496
2.9193-3.21310.28071260.252423462472
3.2131-3.67810.24781290.204923892518
3.6781-4.63390.26941540.178923772531
4.6339-78.9630.23611410.202724982639
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.47810.1882-0.42620.4983-0.29981.28630.0570.04080.0716-0.06350.1864-0.0169-0.15830.0862-0.18290.292-0.0185-0.00740.3296-0.03770.2708-1.519614.5882-24.775
21.4331-0.15730.660.92990.03930.3321-0.0662-0.01-0.0268-0.0739-0.05230.2120.0679-0.12570.07860.27090.05210.00440.351-0.02540.1797-40.626218.9853-19.4826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 240:423A240 - 423
2X-RAY DIFFRACTION2chain A and resid 12:239A12 - 239

+
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