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- PDB-2cjr: Crystal structure of oligomerization domain of SARS coronavirus n... -

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Basic information

Entry
Database: PDB / ID: 2cjr
TitleCrystal structure of oligomerization domain of SARS coronavirus nucleocapsid protein.
ComponentsNUCLEOCAPSID PROTEIN
KeywordsVIRAL PROTEIN / OLIGOMERIZATION DOMAIN / NUCLEOCAPSID PROTEIN / SARS / CORONAVIRUS
Function / homology
Function and homology information


SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / viral capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / molecular adaptor activity / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / host cell nucleus / DNA binding / RNA binding / identical protein binding / plasma membrane
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
Biological speciesSARS CORONAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsChen, C.-Y. / Hsiao, C.-D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Sars Coronavirus Nucleocapsid Protein RNA-Binding Dimerization Domain Suggests a Mechanism for Helical Packaging of Viral RNA.
Authors: Chen, C.-Y. / Chang, C.K. / Chang, Y.W. / Sue, S.C. / Bai, H.I. / Riang, L. / Hsiao, C.-D. / Huang, T.H.
History
DepositionApr 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

Downloads & links

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Assembly

Deposited unit
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN
C: NUCLEOCAPSID PROTEIN
D: NUCLEOCAPSID PROTEIN
E: NUCLEOCAPSID PROTEIN
F: NUCLEOCAPSID PROTEIN
G: NUCLEOCAPSID PROTEIN
H: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)116,4758
Polymers116,4758
Non-polymers00
Water15,385854
1
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,1192
Polymers29,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: NUCLEOCAPSID PROTEIN
D: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,1192
Polymers29,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: NUCLEOCAPSID PROTEIN
F: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,1192
Polymers29,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: NUCLEOCAPSID PROTEIN
H: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,1192
Polymers29,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)159.423, 84.203, 105.177
Angle α, β, γ (deg.)90.00, 131.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NUCLEOCAPSID PROTEIN / OLIGOMERIZATION DOMAIN OF SARS CORONAVIRUS / N STRUCTURAL PROTEIN / NC


Mass: 14559.401 Da / Num. of mol.: 8 / Fragment: RESIDUES 248-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS CORONAVIRUS / Strain: TW1 / Plasmid: PET6H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P59595
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES PRECEDING POSITION 248 OF EACH MONOMER ARE FROM THE HIS-TAG.

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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: 2.4 Å3/Da / Density % sol: 47.7 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: THE STANDARD SPRING-8 ADJUSTABLE-INCLINED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 36262 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.55
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.89 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 92502.96 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: IN CHAIN A,RESIDUES 248-250 ARE DISORDERED. SIDE-CHAINS OF RESIDUE 251 AND 254 ARE INVISIBLE. CHAIN B,RESIDUES 248-252 ARE DISORDERED. SIDE-CHAIN OF RESIDUE 257 IS INVISIBLE. CHAIN ...Details: IN CHAIN A,RESIDUES 248-250 ARE DISORDERED. SIDE-CHAINS OF RESIDUE 251 AND 254 ARE INVISIBLE. CHAIN B,RESIDUES 248-252 ARE DISORDERED. SIDE-CHAIN OF RESIDUE 257 IS INVISIBLE. CHAIN C,RESIDUES 248-252 ARE DISORDERED. SIDE-CHAINS OF RESIDUE 254 AND 257 ARE INVISIBLE. CHAIN D, RESIDUES 248- 250 ARE DISORDERED. SIDE-CHAINS OF RESIDUE 254 AND 257 ARE INVISIBLE. CHAIN E,RESIDUES 248-255 ARE DISORDERED. SIDE- CHAINS OF RESIDUE 257 AND 359 ARE INVISIBLE. CHAIN F, RESIDUES 248-251 ARE DISORDERED. SIDE-CHAINS OF RESIDUE 254 IS INVISIBLE. CHAIN G,RESIDUES 248-254 ARE DISORDERED. CHAIN H,RESIDUES 248-255 ARE DISORDERED. SIDE- CHAINS OF RESIDUE 257, 294, 324, AND 356 ARE INVISIBLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1659 5 %RANDOM
Rwork0.256 ---
obs0.256 33097 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.8828 Å2 / ksol: 0.29568 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.9 Å20 Å20.71 Å2
2--5.02 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7119 0 0 854 7973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
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_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.572
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 221 4.7 %
Rwork0.252 4484 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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