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- PDB-2og3: structure of the rna binding domain of n protein from SARS corona... -

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Basic information

Entry
Database: PDB / ID: 2og3
Titlestructure of the rna binding domain of n protein from SARS coronavirus in cubic crystal form
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / n protein / nucleocapsid / rna binding domain / 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 Tor2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSaikatendu, K. / Joseph, J. / Subramanian, V. / Neuman, B. / Buchmeier, M. / Stevens, R.C. / Kuhn, P.
CitationJournal: J.Virol. / Year: 2007
Title: Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein.
Authors: Saikatendu, K.S. / Joseph, J.S. / Subramanian, V. / Neuman, B.W. / Buchmeier, M.J. / Stevens, R.C. / Kuhn, P.
History
DepositionJan 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)15,3921
Polymers15,3921
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.001, 110.001, 110.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-263-

HOH

21A-365-

HOH

Detailsunknown. forms large homo polymers with genomic and subgenomic rna

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Components

#1: Protein Nucleocapsid protein / N structural protein / NC


Mass: 15392.127 Da / Num. of mol.: 1 / Fragment: rna binding domain of N protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus Tor2 / Genus: Coronavirus / Species: SARS coronavirus / Strain: tor-2 / Gene: N / Plasmid: pmh1-f / Production host: Escherichia coli (E. coli) / Strain (production host): dl41 / References: UniProt: P59595
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 40% MPD and 0.1 M Tris pH 8.0, typically crystals appear within 2 weeks, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å
DetectorDetector: CCD / Date: May 23, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.85→38.9 Å / Num. all: 18018 / Num. obs: 17989 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.068 / Net I/σ(I): 29.33
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.91 / Num. unique all: 1330 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ofz

2ofz


Resolution: 1.85→38.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.243 / SU ML: 0.087 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24711 976 5.1 %RANDOM
Rwork0.19904 ---
all0.1961 17989 --
obs0.20133 17989 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å / Luzzati sigma a obs: 0.197 Å
Refinement stepCycle: LAST / Resolution: 1.85→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 0 243 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022938
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9351283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3775116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2722445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01715129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.427156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02753
X-RAY DIFFRACTIONr_nbd_refined0.2070.2438
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2147
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.235
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_mcbond_it1.0121.5592
X-RAY DIFFRACTIONr_mcangle_it1.6582931
X-RAY DIFFRACTIONr_scbond_it2.2923404
X-RAY DIFFRACTIONr_scangle_it3.6854.5352
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 65 -
Rwork0.281 1330 -
obs--100 %

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