[English] 日本語
Yorodumi
- PDB-6kl5: Structure of The N-terminal domain of Middle East respiratory syn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kl5
TitleStructure of The N-terminal domain of Middle East respiratory syndrome coronavirus Nucleocapsid Protein complexed with Benzyl 2-(Hydroxymethyl)-1-Indolinecarboxylate
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Middle East respiratory syndrome coronavirus / nucleocapsid protein / N-terminal domain / Benzyl 2-(Hydroxymethyl)-1-Indoline carboxylate / VIRUS
Function / homology
Function and homology information


viral RNA genome packaging / negative regulation of interferon-beta production / viral capsid / host cell / viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
Similarity search - Function
Nucleocapsid protein, betacoronavirus / 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
Chem-DJO / N / Nucleoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsHou, M.H. / Lin, S.M. / Hsu, J.N. / Wang, Y.S.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structure-Based Stabilization of Non-native Protein-Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design.
Authors: Lin, S.M. / Lin, S.C. / Hsu, J.N. / Chang, C.K. / Chien, C.M. / Wang, Y.S. / Wu, H.Y. / Jeng, U.S. / Kehn-Hall, K. / Hou, M.H.
History
DepositionJul 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7065
Polymers63,4224
Non-polymers2831
Water00
1
A: Nucleoprotein
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9943
Polymers31,7112
Non-polymers2831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)31,7112
Polymers31,7112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.440, 109.897, 91.526
Angle α, β, γ (deg.)90.000, 101.100, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Nucleoprotein


Mass: 15855.566 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0D3MU65, UniProt: K9N4V7*PLUS
#2: Chemical ChemComp-DJO / (phenylmethyl) (2S)-2-(hydroxymethyl)-2,3-dihydroindole-1-carboxylate / Benzyl 2-(Hydroxymethyl)-1-Indolinecarboxylate


Mass: 283.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
22.7655.4
1
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5 mg/mL protein, 25 mM Tris-HCl, pH 7.5, 75 mM NaCl, 70 mM MES, pH5.5, 37.5 M (NH4)2SO4, 14.5 % PEG 3350, 1 mM NaBr, 1mM

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 3.076→30 Å / Num. obs: 12334 / % possible obs: 96.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.084 / Rrim(I) all: 0.161 / Χ2: 0.928 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.09-3.23.40.48112660.7880.2980.5670.83996.9
3.2-3.333.50.37612230.8160.230.4410.96296.8
3.33-3.483.50.32812270.860.20.3851.01996.6
3.48-3.663.50.25412180.9110.1540.2981.00795.1
3.66-3.893.50.18612260.940.1140.2191.05695.6
3.89-4.193.50.14511850.9750.0880.171.02294
4.19-4.613.50.10912110.9840.0670.1281.00493.5
4.61-5.283.50.08412120.9910.0510.0990.93294.5
5.28-6.643.50.0712560.9910.0430.0820.7898.4
6.64-6.643.70.04213100.9960.0260.050.70499.1

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data collection
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3K

4j3k


Resolution: 3.09→26.289 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 30.29
RfactorNum. reflection% reflection
Rfree0.2988 1184 9.93 %
Rwork0.2811 --
obs0.2829 11927 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.65 Å2 / Biso mean: 54.0869 Å2 / Biso min: 24.13 Å2
Refinement stepCycle: final / Resolution: 3.09→26.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 21 0 3498
Biso mean--45.41 --
Num. residues----445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Rfactor Rwork: 0.2594

Resolution (Å)Rfactor RfreeNum. reflection RfreeNum. reflection Rwork% reflection obs (%)
3.09-3.21540.3943127114078
3.2154-3.38460.3224140128891
3.3846-3.59610.297148136694
3.5961-3.8730.2989157136896
3.873-4.26130.3158152133694
4.2613-4.87450.2594148136994
4.8745-6.12850.2749156141297
6.1285-6.12850.3087156146499

+
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