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- PDB-4li4: Crystal structure of HCoV-OC43 N-NTD complexed with AMP -

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Basic information

Entry
Database: PDB / ID: 4li4
TitleCrystal structure of HCoV-OC43 N-NTD complexed with AMP
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / RNA-binding / AMP / Coronavirus / Nucleocapsid protein / N-terminal domain
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
ADENOSINE MONOPHOSPHATE / Nucleoprotein / Nucleocapsid protein
Similarity search - Component
Biological speciesHuman coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 2, 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)15,7852
Polymers15,4381
Non-polymers3471
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.919, 81.919, 42.893
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: 15437.901 Da / Num. of mol.: 1 / Fragment: UNP residues 55-188
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M SPG, 25% PEG1500, 5mM AMP, 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: 1.71→30 Å / Num. obs: 17535 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.46 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.03
Reflection shellHighest resolution: 1.71 Å / % possible all: 97.8

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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: 1.71→26.814 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7822 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 1426 8.15 %RANDOM
Rwork0.2486 ---
obs0.2499 17501 97.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.63 Å2 / Biso mean: 30.6922 Å2 / Biso min: 11.03 Å2
Refinement stepCycle: LAST / Resolution: 1.71→26.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 23 126 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181136
X-RAY DIFFRACTIONf_angle_d2.2281557
X-RAY DIFFRACTIONf_chiral_restr0.09151
X-RAY DIFFRACTIONf_plane_restr0.025204
X-RAY DIFFRACTIONf_dihedral_angle_d15.181397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7101-1.77120.34511430.298516131756100
1.7712-1.84210.32861480.306216391787100
1.8421-1.92590.28421470.302616261773100
1.9259-2.02740.28311430.300216321775100
2.0274-2.15440.28141490.276516461795100
2.1544-2.32060.29011280.27461445157389
2.3206-2.5540.32961470.26316421789100
2.554-2.92320.27421460.252816491795100
2.9232-3.68140.23521390.23311587172696
3.6814-26.81760.22761360.21081596173294

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