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- PDB-6kl2: Structure of the N-terminal domain of Middle East respiratory syn... -

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Basic information

Entry
Database: PDB / ID: 6kl2
TitleStructure of the N-terminal domain of Middle East respiratory syndrome coronavirus nucleocapsid protein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Middle East respiratory syndrome coronavirus / nucleocapsid protein / N-terminal domain
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
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsHou, M.H. / Wang, Y.S. / Lin, S.M. / 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


Theoretical massNumber of molelcules
Total (without water)63,4224
Polymers63,4224
Non-polymers00
Water1,820101
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


Theoretical massNumber of molelcules
Total (without water)31,7112
Polymers31,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.601, 109.645, 91.993
Angle α, β, γ (deg.)90.000, 101.230, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.7 %
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

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.627→30 Å / Num. obs: 19546 / % possible obs: 94.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.038 / Rrim(I) all: 0.103 / Χ2: 0.886 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.63-2.725.90.49318720.8410.2160.540.86691.4
2.72-2.836.70.45319070.8970.1880.4920.86593.2
2.83-2.967.20.32819390.9550.130.3530.91791.9
2.96-3.127.40.24418590.9710.0950.2620.95792.4
3.12-3.317.30.16318990.9830.0630.1750.99992.1
3.31-3.577.20.12319680.9890.0480.1321.00293.8
3.57-3.937.10.08219600.9930.0320.0880.95296.1
3.93-4.497.10.05520380.9960.0220.060.82897.9
4.49-5.657.40.04920380.9970.0190.0520.79898.9
5.65-307.40.03720660.9980.0140.040.69897.5

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Processing

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

4j3k


Resolution: 2.63→23.472 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.2898 1915 9.97 %
Rwork0.28 --
obs0.281 19199 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.11 Å2 / Biso mean: 40.5667 Å2 / Biso min: 19.32 Å2
Refinement stepCycle: final / Resolution: 2.63→23.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 0 101 3546
Biso mean---37.87 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133570
X-RAY DIFFRACTIONf_angle_d1.594898
X-RAY DIFFRACTIONf_dihedral_angle_d10.232034
X-RAY DIFFRACTIONf_chiral_restr0.079505
X-RAY DIFFRACTIONf_plane_restr0.011646
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.63-2.69290.26211110.247199375
2.6929-2.76560.3745126114686
2.7656-2.84680.33011390.2471118792
2.8468-2.93850.35981410.2471123192
2.9385-3.04330.30561370.2471121393
3.0433-3.16490.30831280.2471120391
3.1649-3.30860.29071340.2471124393
3.3086-3.48250.2671280.2471124193
3.4825-3.69990.26931410.2471126596
3.6999-3.98430.27931450.2471130196
3.9843-4.38290.3031450.2471131298
4.3829-5.01170.24711420.2471128999
5.0117-6.2940.25161460.2471132199

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