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- PDB-8w6w: Crystal Structure of C-terminal domain of nucleocapsid protein fr... -

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Basic information

Entry
Database: PDB / ID: 8w6w
TitleCrystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ampicillin
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 ...: / 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 / 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
Chem-AIC / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5504
Polymers39,1382
Non-polymers4112
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-33 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.582, 43.604, 56.762
Angle α, β, γ (deg.)90.00, 108.66, 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: 19569.055 Da / Num. of mol.: 2 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID


Mass: 349.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 1.64 Å3/Da / Density % sol: 25.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG4000, 0.2 M Lithium sulfate, 50 mM Tris pH 8.0, Ampicillin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→24.17 Å / Num. obs: 10644 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.993 / Net I/σ(I): 29.4
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 910 / CC1/2: 0.981

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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: 2.2→24.17 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.876 / SU B: 10.953 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23827 486 4.6 %RANDOM
Rwork0.17964 ---
obs0.18225 10145 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.223 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.11 Å2
2---0.18 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.2→24.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 28 230 1985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0111812
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161680
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.6832455
X-RAY DIFFRACTIONr_angle_other_deg0.5051.593865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5385216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.98514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35510296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
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_it0.8680.982867
X-RAY DIFFRACTIONr_mcbond_other0.8580.982867
X-RAY DIFFRACTIONr_mcangle_it1.4861.7561082
X-RAY DIFFRACTIONr_mcangle_other1.4851.761083
X-RAY DIFFRACTIONr_scbond_it1.4351.253945
X-RAY DIFFRACTIONr_scbond_other1.4351.254946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3812.221372
X-RAY DIFFRACTIONr_long_range_B_refined5.11613.552259
X-RAY DIFFRACTIONr_long_range_B_other4.89412.492207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 50 -
Rwork0.184 718 -
obs--100 %
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)
10.2762-0.0436-0.03250.67020.00460.2481-0.0308-0.0149-0.03690.0236-0.00610.0133-0.0114-0.0080.03680.0130.00470.00010.02380.00230.01028.5975-5.67658.909
20.1096-0.22870.01450.75330.09960.2982-0.01280.01-0.00110.0891-0.0064-0.0222-0.01170.00330.01920.0215-0.0012-0.01070.04030.00440.00719.3726.344415.8245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 301
2X-RAY DIFFRACTION2B11 - 301

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