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- PDB-4lm9: Crystal structure of HCoV-OC43 N-NTD complexed with GMP -

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Basic information

Entry
Database: PDB / ID: 4lm9
TitleCrystal structure of HCoV-OC43 N-NTD complexed with GMP
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
GUANOSINE-5'-MONOPHOSPHATE / Nucleoprotein / Nucleocapsid protein
Similarity search - Component
Biological speciesHuman coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7142
Polymers15,3511
Non-polymers3631
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.971, 81.971, 42.732
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-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 54.44 %
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: 1.6→30 Å / Num. all: 144518 / Num. obs: 144518 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.55 Å2
Reflection shellResolution: 1.6→1.63 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3K

4j3k


Resolution: 1.601→23.663 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7766 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 29.12 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 2001 9.92 %RANDOM
Rwork0.2257 ---
obs0.2303 20172 97.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.65 Å2 / Biso mean: 21.0455 Å2 / Biso min: 1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.601→23.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 24 143 1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131131
X-RAY DIFFRACTIONf_angle_d1.5891551
X-RAY DIFFRACTIONf_chiral_restr0.087150
X-RAY DIFFRACTIONf_plane_restr0.007204
X-RAY DIFFRACTIONf_dihedral_angle_d15.127404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6009-1.6410.31741000.342488498432
1.641-1.68530.33931180.32031067118540
1.6853-1.73490.34521490.31741320146949
1.7349-1.79090.28211490.3241409155851
1.7909-1.85490.36211540.32411405155951
1.8549-1.92910.351460.32861316146249
1.9291-2.01680.34341490.25641377152651
2.0168-2.12310.29421530.21561401155451
2.1231-2.2560.28351380.21651237137545
2.256-2.43010.29791380.21281261139946
2.4301-2.67430.27961520.21221392154452
2.6743-3.06060.22521530.20191415156852
3.0606-3.85330.23131440.17721269141347
3.8533-23.66560.22071580.17881418157652

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