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- PDB-8zfv: Crystal Structure of C-terminal domain of nucleocapsid protein fr... -

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Basic information

Entry
Database: PDB / ID: 8zfv
TitleCrystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone
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 / Maturation of nucleoprotein / poly(U) RNA binding / 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 / Maturation of nucleoprotein / poly(U) RNA binding / 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 / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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
Ceftriaxone / DI(HYDROXYETHYL)ETHER / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMay 8, 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
C: Nucleoprotein
B: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1429
Polymers78,2764
Non-polymers1,8665
Water12,052669
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3435
Polymers39,1382
Non-polymers1,2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-32 kcal/mol
Surface area12920 Å2
MethodPISA
2
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7994
Polymers39,1382
Non-polymers6612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-28 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.539, 46.643, 69.021
Angle α, β, γ (deg.)106.66, 90.11, 93.46
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 19569.055 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-9F2 / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C18H18N8O7S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
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: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→26.58 Å / Num. obs: 34801 / % possible obs: 99.2 % / Redundancy: 4.2 % / CC1/2: 0.997 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2572 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YUN

6yun


Resolution: 2→26.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.392 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20494 1752 5 %RANDOM
Rwork0.14731 ---
obs0.15019 33047 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.983 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0.03 Å2-0.12 Å2
2--1.07 Å20.34 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→26.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 120 669 4337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123856
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163545
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.8385230
X-RAY DIFFRACTIONr_angle_other_deg0.6621.7978169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.586555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03510636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.5510.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02953
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_it1.2951.3211821
X-RAY DIFFRACTIONr_mcbond_other1.291.3211821
X-RAY DIFFRACTIONr_mcangle_it2.0862.3622285
X-RAY DIFFRACTIONr_mcangle_other2.0862.3632286
X-RAY DIFFRACTIONr_scbond_it2.3651.7692035
X-RAY DIFFRACTIONr_scbond_other2.3651.7692036
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8353.0932940
X-RAY DIFFRACTIONr_long_range_B_refined6.4721.924866
X-RAY DIFFRACTIONr_long_range_B_other6.4721.924867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 119 -
Rwork0.194 2444 -
obs--98.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4696-0.20840.01520.1381-0.06160.3189-0.0426-0.016-0.00690.00110.0123-0.0195-0.01160.00640.03030.0204-0.00270.0010.002-0.00170.022216.8053-9.73226.5349
20.70790.1263-0.06520.2569-0.06860.0396-0.055-0.05840.0239-0.02060.0362-0.01630.01470.00440.01880.00770.00570.00540.01970.00140.0163-5.16679.306-8.1763
30.59910.1821-0.12950.08470.00010.4942-0.0325-0.0944-0.0945-0.0262-0.0442-0.0305-0.0156-0.0230.07670.01670.00780.00420.02980.01440.0244.9242-16.894318.9813
40.4869-0.2606-0.07380.23890.03860.4341-0.01780.06750.06650.0227-0.0357-0.0196-0.01340.01050.05340.0083-0.00430.00330.01060.01120.0279-16.832717.4623-18.3235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A251 - 794
2X-RAY DIFFRACTION2C257 - 652
3X-RAY DIFFRACTION3B253 - 656
4X-RAY DIFFRACTION4D254 - 771

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