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- PDB-4lmc: Crystal structure of HCoV-OC43 N-NTD complexed with CMP -

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Basic information

Entry
Database: PDB / ID: 4lmc
TitleCrystal structure of HCoV-OC43 N-NTD complexed with CMP
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / HCoV-OC43 / Nucleocapsid protein / N-terminal domain / RNA binding
Function / homology
Function and homology information


host cell / viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
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
CYTIDINE-5'-MONOPHOSPHATE / Nucleoprotein / Nucleocapsid protein
Similarity search - Component
Biological speciesHuman coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.742 Å
AuthorsLin, S.Y. / Liu, C.L. / Hou, M.H.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target
Authors: Lin, S.Y. / Liu, C.L. / Chang, Y.M. / Zhao, J. / Perlman, S. / Hou, M.H.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6742
Polymers15,3511
Non-polymers3231
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.897, 81.897, 42.889
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nucleoprotein


Mass: 15350.822 Da / Num. of mol.: 1 / Fragment: UNP residues 55-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus / Strain: OC43 / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SA23, UniProt: P33469*PLUS
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG1500, 0.25M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→30 Å / Num. all: 16152 / Num. obs: 16152 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.72 Å2
Reflection shellResolution: 1.74→1.8 Å / % possible all: 94.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3K

4j3k


Resolution: 1.742→26.807 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8157 / SU ML: 0.21 / σ(F): 1.37 / Phase error: 25.42 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 1628 10.09 %Random
Rwork0.2175 ---
all0.2195 ---
obs0.2212 16137 95.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.81 Å2 / Biso mean: 33.1738 Å2 / Biso min: 11.27 Å2
Refinement stepCycle: LAST / Resolution: 1.742→26.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 21 118 1204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141127
X-RAY DIFFRACTIONf_angle_d1.5771544
X-RAY DIFFRACTIONf_chiral_restr0.328150
X-RAY DIFFRACTIONf_plane_restr0.008203
X-RAY DIFFRACTIONf_dihedral_angle_d14.625395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7424-1.79360.29521340.283312501384100
1.7936-1.85150.28521430.2812641407100
1.8515-1.91770.32291350.261241137699
1.9177-1.99440.2991450.235412601405100
1.9944-2.08510.25821420.217312601402100
2.0851-2.1950.28541410.226312571398100
2.195-2.33250.25471130.2138980109378
2.3325-2.51250.25081420.217412731415100
2.5125-2.76510.23521400.212812591399100
2.7651-3.16460.23571450.214712671412100
3.1646-3.9850.25621210.19111083120484
3.985-26.81020.22891270.21781115124284

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