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- PDB-8k75: N-terminal domain of FIPV nucleocapsid protein -

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Basic information

Entry
Database: PDB / ID: 8k75
TitleN-terminal domain of FIPV nucleocapsid protein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / FIPV / Nucleocapsid protein
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Nucleocapsid protein, alphacoronavirus / 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 speciesFeline coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å
AuthorsZhang, J.T. / Liang, R. / Shi, Y.J. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Identification of novel broad-spectrum antiviral drugs targeting the N-terminal domain of the FIPV nucleocapsid protein.
Authors: Zhang, J. / Fan, X. / Wang, P. / Liang, R. / Wang, D. / Xu, J. / Zhang, D. / Xie, Y. / Liao, Q. / Jiao, Z. / Shi, Y. / Peng, G.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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


Theoretical massNumber of molelcules
Total (without water)16,6191
Polymers16,6191
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.768, 60.900, 35.621
Angle α, β, γ (deg.)90.00, 97.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16618.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline coronavirus (strain FIPV WSU-79/1146)
Gene: N, 6 / Production host: Escherichia coli (E. coli) / References: UniProt: P25909
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. obs: 41565 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Χ2: 1.19 / Net I/σ(I): 7.1 / Num. measured all: 270478
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.16-1.185.20.18719720.9780.9940.0880.2071.08194.8
1.18-1.25.60.19120430.9760.9940.0860.211.27497.5
1.2-1.2260.19220230.9750.9940.0820.2091.39297.7
1.22-1.256.60.1820670.9790.9950.0730.1941.37398.2
1.25-1.286.40.17320560.9840.9960.0720.1881.29899
1.28-1.316.80.16120870.9850.9960.0640.1741.28398.4
1.31-1.346.70.15820260.9860.9970.0640.171.2598.7
1.34-1.386.40.14621050.9840.9960.060.1581.1698.8
1.38-1.426.60.13620600.9870.9970.0550.1471.20899.5
1.42-1.466.50.12320830.9910.9980.0510.1331.13999.3
1.46-1.516.80.11120900.990.9970.0450.121.30799.5
1.51-1.576.70.10820740.990.9980.0440.1161.11699.5
1.57-1.656.40.09520900.9930.9980.040.1031.23299.5
1.65-1.736.70.08620940.9940.9990.0350.0931.02899.8
1.73-1.846.80.0820940.9950.9990.0320.0861.101100
1.84-1.986.90.06921140.9960.9990.0280.0750.983100
1.98-2.186.60.05921050.9970.9990.0240.0640.774100
2.18-2.56.80.04921040.9980.9990.020.0530.814100
2.5-3.156.90.03921160.9980.9990.0160.0430.741100
3.15-506.70.05321620.9930.9980.0220.0572.26699.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.16→30.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.49 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18383 2006 4.8 %RANDOM
Rwork0.16761 ---
obs0.1684 39396 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.049 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.01 Å2
2---0.02 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.16→30.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 190 1213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151007
X-RAY DIFFRACTIONr_angle_refined_deg1.821.6561421
X-RAY DIFFRACTIONr_angle_other_deg1.4291.5922315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1945123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.14421.42963
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57115183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.281159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
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_it1.4151.46495
X-RAY DIFFRACTIONr_mcbond_other1.3691.456494
X-RAY DIFFRACTIONr_mcangle_it2.092.192617
X-RAY DIFFRACTIONr_mcangle_other2.0882.197618
X-RAY DIFFRACTIONr_scbond_it2.4841.734558
X-RAY DIFFRACTIONr_scbond_other2.4311.725556
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.592.488804
X-RAY DIFFRACTIONr_long_range_B_refined5.23518.4651206
X-RAY DIFFRACTIONr_long_range_B_other4.75717.2031150
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.161→1.191 Å
RfactorNum. reflection% reflection
Rfree0.219 122 -
Rwork0.219 2723 -
obs--91.95 %

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