[English] 日本語
Yorodumi
- PDB-5epw: C-Terminal Domain Of Human Coronavirus Nl63 Nucleocapsid Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5epw
TitleC-Terminal Domain Of Human Coronavirus Nl63 Nucleocapsid Protein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / NL63 coronavirus / N-protein / C-Terminal Domain
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / host cell cytoplasm / ribonucleoprotein complex / DNA binding / RNA binding
Similarity search - Function
Nucleocapsid protein, alphacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
Biological speciesHuman coronavirus NL63
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSzelazek, B. / Kabala, W. / Kus, K. / Zdzalik, M. / Golik, P. / Florek, D. / Burmistrz, M. / Pyrc, K. / Dubin, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science CenterUMO-2011/01/D/NZ1/01169 Poland
CitationJournal: J. Virol. / Year: 2017
Title: Structural Characterization of Human Coronavirus NL63 N Protein.
Authors: Szelazek, B. / Kabala, W. / Kus, K. / Zdzalik, M. / Twarda-Clapa, A. / Golik, P. / Burmistrz, M. / Florek, D. / Wladyka, B. / Pyrc, K. / Dubin, G.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3May 8, 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


Theoretical massNumber of molelcules
Total (without water)29,5512
Polymers29,5512
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-37 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.290, 68.290, 92.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 14775.406 Da / Num. of mol.: 2 / Fragment: CTD, UNP residues 221-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus NL63 / Gene: N, 6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q1R8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M PCTP pH 8.0, 25% PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.5→49.83 Å / Num. all: 399891 / Num. obs: 39167 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.337 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19768 1961 5 %RANDOM
Rwork0.16857 ---
obs0.17008 37156 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.307 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: 1 / Resolution: 1.5→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 0 216 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021780
X-RAY DIFFRACTIONr_bond_other_d0.0020.021686
X-RAY DIFFRACTIONr_angle_refined_deg2.3951.9552420
X-RAY DIFFRACTIONr_angle_other_deg1.19833900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.4526.08792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95615314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.195157
X-RAY DIFFRACTIONr_chiral_restr0.1580.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212065
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3011.899868
X-RAY DIFFRACTIONr_mcbond_other2.3011.898867
X-RAY DIFFRACTIONr_mcangle_it3.1932.8431085
X-RAY DIFFRACTIONr_mcangle_other3.1922.8441086
X-RAY DIFFRACTIONr_scbond_it3.2082.163912
X-RAY DIFFRACTIONr_scbond_other3.22.16909
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7423.1181327
X-RAY DIFFRACTIONr_long_range_B_refined5.93515.6622132
X-RAY DIFFRACTIONr_long_range_B_other5.83115.0962027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 140 -
Rwork0.246 2765 -
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