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- PDB-6kl6: Crystal structure of MERS-CoV N-NTD complexed with 5-Benzyloxygramine -

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Basic information

Entry
Database: PDB / ID: 6kl6
TitleCrystal structure of MERS-CoV N-NTD complexed with 5-Benzyloxygramine
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Middle East respiratory syndrome coronavirus / nucleocapsid protein / N-terminal domain / 5-BENZYLOXYGRAMINE
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 / viral nucleocapsid / 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-DJU / N / Nucleoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsHou, M.H. / Lin, S.M. / Wang, Y.S. / Hsu, J.N.
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)63,7035
Polymers63,4224
Non-polymers2801
Water1,982110
1
A: Nucleoprotein
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)31,7112
Polymers31,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9913
Polymers31,7112
Non-polymers2801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.489, 108.477, 91.595
Angle α, β, γ (deg.)90.000, 101.160, 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-DJU / N,N-dimethyl-1-(5-phenylmethoxy-1H-indol-3-yl)methanamine / 5-Benzyloxygramine


Mass: 280.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.9 %
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, 1 mM 5-Benzyloxygramine

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.76→30 Å / Num. obs: 17388 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Χ2: 0.939 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.77-2.877.30.47717010.9220.190.5141.15899.4
2.87-2.987.20.32417520.9590.1290.3491.12499.4
2.98-3.126.80.21816700.980.090.2360.91899.3
3.12-3.286.50.14317820.9890.060.1560.90698.9
3.28-3.496.40.11117180.9910.0480.1210.93899.6
3.49-3.766.20.07517360.9940.0330.0830.97499.6
3.76-4.146.30.05217330.9960.0230.0570.965100
4.14-4.736.40.0417680.9960.0170.0440.88699.9
4.73-5.955.80.03217660.9970.0150.0350.69899.9

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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: 2.77→29.394 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 25.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 1742 10.03 %RANDOM
Rwork0.2315 ---
obs0.2354 17363 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.2 Å2 / Biso mean: 35.3863 Å2 / Biso min: 9.9 Å2
Refinement stepCycle: final / Resolution: 2.77→29.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 41 110 3700
Biso mean--41.89 32.26 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083698
X-RAY DIFFRACTIONf_angle_d1.3395064
X-RAY DIFFRACTIONf_dihedral_angle_d2.9932102
X-RAY DIFFRACTIONf_chiral_restr0.056519
X-RAY DIFFRACTIONf_plane_restr0.008663
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.77-2.84150.33691410.2102124095
2.8415-2.93320.31871440.2102129299
2.9332-3.03790.33311410.2102129099
3.0379-3.15940.30651480.2102131699
3.1594-3.3030.27361410.2102128599
3.303-3.47690.28681410.21021302100
3.4769-3.69440.29511480.21021298100
3.6944-3.9790.2631470.21021339100
3.979-4.37820.24681480.21021313100
4.3782-5.0090.21021440.20671324100
5.009-6.30060.24961480.21021294100

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