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- PDB-6kl5: Structure of The N-terminal domain of Middle East respiratory syn... -

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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 endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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