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- PDB-4j3k: Structure of the N-terminal domian of human coronavirus OC43 nucl... -

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Basic information

Entry
Database: PDB / ID: 4j3k
TitleStructure of the N-terminal domian of human coronavirus OC43 nucleocapsid protein
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / five-stranded beta-sheet / long extended loop / RNA-binding
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, betacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
Nucleoprotein / Nucleocapsid protein
Similarity search - Component
Biological speciesHuman coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, I.J. / Lin, S.Y. / Hou, M.H.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein
Authors: Chen, I.J. / Yuann, J.M. / Chang, Y.M. / Lin, S.Y. / Zhao, J. / Perlman, S. / Shen, Y.Y. / Huang, T.H. / Hou, M.H.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 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)15,5602
Polymers15,4381
Non-polymers1221
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.570, 81.570, 42.550
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SA23, UniProt: P33469*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG1500, 0.25M SPG, 225mM NaCl, 50mM Tris-HCl, 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: Jul 25, 2009
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: 2→30 Å / Num. all: 11131 / Num. obs: 11131 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.07 Å / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ofz

2ofz


Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 559 5.1 %RANDOM
Rwork0.2007 ---
all0.2013 11055 --
obs0.2013 10904 98.6 %-
Solvent computationBsol: 48.2968 Å2
Displacement parametersBiso mean: 27.0347 Å2
Baniso -1Baniso -2Baniso -3
1-0.402 Å2-0.686 Å20 Å2
2--0.402 Å20 Å2
3----0.803 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 8 157 1236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0137
X-RAY DIFFRACTIONc_angle_deg1.978

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