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- PDB-9in1: Crystal Structure of C-terminal domain of nucleocapsid protein fr... -

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Basic information

Entry
Database: PDB / ID: 9in1
TitleCrystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucleocapsid protein / RNA binding C-terminal domain / drugs
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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...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 / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDhaka, P. / Mahto, J.K. / Tomar, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST-SERB IPA/2020/000054 India
CitationJournal: J.Struct.Biol. / Year: 2025
Title: Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
Authors: Dhaka, P. / Mahto, J.K. / Singh, A. / Kumar, P. / Tomar, S.
History
DepositionJul 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)53,7934
Polymers53,7934
Non-polymers00
Water14,970831
1
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,8962
Polymers26,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-29 kcal/mol
Surface area11440 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,8962
Polymers26,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-31 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.045, 43.486, 74.785
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13448.181 Da / Num. of mol.: 4 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG4000, 0.2 M Lithium sulfate, 50 mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.4→27.46 Å / Num. obs: 85007 / % possible obs: 94.4 % / Redundancy: 3.7 % / CC1/2: 0.999 / Net I/σ(I): 17.2
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 3753 / CC1/2: 0.832

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YUN

6yun


Resolution: 1.4→24.05 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.129 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16963 4160 4.9 %RANDOM
Rwork0.13205 ---
obs0.13388 80831 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.752 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.35 Å2
2---0.9 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.4→24.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 0 831 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123880
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163664
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.8365262
X-RAY DIFFRACTIONr_angle_other_deg0.6961.7998472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5565492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.018526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8310680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02960
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_it3.4410.9521885
X-RAY DIFFRACTIONr_mcbond_other3.4240.9511885
X-RAY DIFFRACTIONr_mcangle_it5.3251.6992368
X-RAY DIFFRACTIONr_mcangle_other5.331.72369
X-RAY DIFFRACTIONr_scbond_it4.5171.1541995
X-RAY DIFFRACTIONr_scbond_other4.5171.1551996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6862.0022882
X-RAY DIFFRACTIONr_long_range_B_refined17.25116.944923
X-RAY DIFFRACTIONr_long_range_B_other14.28212.454643
X-RAY DIFFRACTIONr_rigid_bond_restr3.6537544
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å
RfactorNum. reflection% reflection
Rfree0.257 306 -
Rwork0.203 5436 -
obs--87.24 %

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