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- PDB-4lm7: Crystal structure of HCoV-OC43 N-NTD complexed with UMP -

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Basic information

Entry
Database: PDB / ID: 4lm7
TitleCrystal structure of HCoV-OC43 N-NTD complexed with UMP
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / Nucleocapsid protein / N-terminal domain / RNA binding
Function / homology
Function and homology information


host cell / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / 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
URIDINE-5'-MONOPHOSPHATE / Nucleoprotein / Nucleocapsid protein
Similarity search - Component
Biological speciesHuman coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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)15,7622
Polymers15,4381
Non-polymers3241
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.940, 81.940, 42.820
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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 54.24 %

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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: 1.72→30 Å / Num. all: 122776 / Num. obs: 122776 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.72→1.78 Å / % possible all: 100

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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: 1.72→22.73 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8053 / SU ML: 0.18 / σ(F): 1.38 / Phase error: 26.37 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 1404 8.07 %RAMDOM
Rwork0.2246 ---
obs0.2271 17396 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.21 Å2 / Biso mean: 29.5923 Å2 / Biso min: 12.82 Å2
Refinement stepCycle: LAST / Resolution: 1.72→22.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 21 165 1257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171133
X-RAY DIFFRACTIONf_angle_d1.721552
X-RAY DIFFRACTIONf_chiral_restr0.105151
X-RAY DIFFRACTIONf_plane_restr0.009205
X-RAY DIFFRACTIONf_dihedral_angle_d15.354397
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 (%)
1.72-1.78150.31071390.262316391778100
1.7815-1.85280.28031410.277716011742100
1.8528-1.93710.29381390.266315831722100
1.9371-2.03910.25681450.249316101755100
2.0391-2.16680.28051390.243315961735100
2.1668-2.33390.27491470.23216201767100
2.3339-2.56850.28121470.229316211768100
2.5685-2.93950.24111390.216216011740100
2.9395-3.70090.2371400.20231633177399
3.7009-22.73230.23541280.21521488161689

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