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- PDB-2bxx: Crystal structure of the N-terminal domain of IBV coronavirus nuc... -

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Basic information

Entry
Database: PDB / ID: 2bxx
TitleCrystal structure of the N-terminal domain of IBV coronavirus nucleocapsid. Native crystal form
ComponentsNUCLEOCAPSID PROTEINVirus
KeywordsNUCLEOCAPSID PROTEIN / PHOSPHORYLATION / RNA-BINDING / VIRAL NUCLEOPROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding / identical protein binding
Similarity search - Function
Nucleocapsid protein, gammacoronavirus / 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, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesAVIAN INFECTIOUS BRONCHITIS VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFan, H. / Ooi, A. / Liu, D.-X. / Lescar, J.
CitationJournal: Structure / Year: 2005
Title: The Nucleocapsid Protein of Coronavirus Infectious Bronchitis Virus: Crystal Structure of its N-Terminal Domain and Multimerization Properties.
Authors: Fan, H. / Ooi, A. / Tan, Y.W. / Wang, S. / Fang, S. / Liu, D.-X. / Lescar, J.
History
DepositionJul 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,0292
Polymers30,0292
Non-polymers00
Water3,369187
1
A: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0151
Polymers15,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0151
Polymers15,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.422, 35.776, 55.860
Angle α, β, γ (deg.)99.20, 94.07, 108.96
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.376, -0.927, 0.003), (-0.926, -0.376, -0.027), (0.026, 0.007, -1)
Vector: 1.56722, -3.17674, 16.0061)

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Components

#1: Protein NUCLEOCAPSID PROTEIN / Virus / INFECTIOUS BRONCHITIS VIRUS NUCLEOCAPSID PROTEIN / N STRUCTURAL PROTEIN / NC


Mass: 15014.549 Da / Num. of mol.: 2 / Fragment: RNA BINDING DOMAIN RESIDUES 29-160 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN INFECTIOUS BRONCHITIS VIRUS / Strain: BEAUDETTE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P69597, UniProt: P69596*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 85 TO CYS ENGINEERED RESIDUE IN CHAIN B, LYS 85 TO CYS
Sequence detailsENGINEERED MUTATION AT POSITION 85

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.62 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Dec 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 20031 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.1 / % possible all: 88.8

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BTL

2btl


Resolution: 1.85→19.92 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKEIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27033 1026 5.1 %RANDOM
Rwork0.22963 ---
obs0.22963 18921 92.4 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.284 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å22.18 Å21.45 Å2
2--0.32 Å21.22 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 0 187 2317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.05
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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