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- PDB-9f2h: Crystal structure of SARS-CoV-2 N-protein C-terminal domain in co... -

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Basic information

Entry
Database: PDB / ID: 9f2h
TitleCrystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / CTD / SARS-CoV-2 nucleocapsid / COVID-19 / riluzole / benzothiazols
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
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
6-(trifluoromethoxy)-1,3-benzothiazol-2-amine / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMarquez-Monino, M.A. / Gonzalez, B. / Perez-Canadillas, J.M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117400GB-100 Spain
Spanish Ministry of Science, Innovation, and UniversitiesMCIN/AEI/10.13039/501100011033 Spain
CitationJournal: Structure / Year: 2025
Title: The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.
Authors: Marquez-Monino, M.A. / Santiveri, C.M. / de Leon, P. / Camero, S. / Campos-Olivas, R. / Jimenez, M.A. / Saiz, M. / Gonzalez, B. / Perez-Canadillas, J.M.
History
DepositionApr 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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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)50,6979
Polymers50,1124
Non-polymers5845
Water11,277626
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4835
Polymers25,0562
Non-polymers4263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-42 kcal/mol
Surface area11510 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2144
Polymers25,0562
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-32 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.056, 43.383, 109.326
Angle α, β, γ (deg.)90.00, 91.44, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 12528.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C-terminal domain. Initial GS are expression tags.
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pET28-txAHEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9
#2: Chemical ChemComp-657 / 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine / Riluzole


Mass: 234.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H5F3N2OS / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.05 % / Description: Rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350 38%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate and 1 mM InsP6. Protein:precipitant ratio 1:1. Protein concentration: 16.5 mg/ml. Protein buffer: 20 mM Tris pH 8.0 and 150 mM NaCl. ...Details: PEG 3350 38%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate and 1 mM InsP6. Protein:precipitant ratio 1:1. Protein concentration: 16.5 mg/ml. Protein buffer: 20 mM Tris pH 8.0 and 150 mM NaCl. Soaking o/n with saturated concentration of riluzole in PEG 3350 40%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate, 1 mM InsP6 condition.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.774899 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jul 10, 2021 / Details: Toroidal mirror, elliptical beam shape
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.774899 Å / Relative weight: 1
ReflectionResolution: 1.3→46.56 Å / Num. obs: 103602 / % possible obs: 97 % / Redundancy: 5.5 % / Biso Wilson estimate: 14.431 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 12.3
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4726 / CC1/2: 0.685 / Rpim(I) all: 0.363 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→46.56 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.851 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18898 5140 5 %RANDOM
Rwork0.1675 ---
obs0.16856 98450 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.38 Å2
2---0.23 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.3→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 34 628 4150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123841
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163573
X-RAY DIFFRACTIONr_angle_refined_deg1.361.6695220
X-RAY DIFFRACTIONr_angle_other_deg0.4781.5868243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.485531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08110659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
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_it1.2961.6751850
X-RAY DIFFRACTIONr_mcbond_other1.2951.6751850
X-RAY DIFFRACTIONr_mcangle_it2.0662.9972344
X-RAY DIFFRACTIONr_mcangle_other2.0662.9972345
X-RAY DIFFRACTIONr_scbond_it1.9221.9891991
X-RAY DIFFRACTIONr_scbond_other1.9221.991992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0693.5222877
X-RAY DIFFRACTIONr_long_range_B_refined4.71121.664761
X-RAY DIFFRACTIONr_long_range_B_other4.38418.444519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 344 -
Rwork0.256 6822 -
obs--90.89 %

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