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- PDB-2ofz: Ultrahigh Resolution Crystal Structure of RNA Binding Domain of S... -

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Basic information

Entry
Database: PDB / ID: 2ofz
TitleUltrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / SARS CORONAVIRUS NUCLEOCAPSID RNA BINDING N-TERMINAL DOMAIN / N PROTEIN / SARS-ORF9A
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: 1.17 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 4, 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 ...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: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4542
Polymers15,3921
Non-polymers621
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.571, 36.440, 47.737
Angle α, β, γ (deg.)90.00, 94.71, 90.00
Int Tables number4
Space group name H-MP1211

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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 SARS NUCLEOCAPSID
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 25% PEG 2000MME, 0.2 M sodium bromide, 0.1 M sodium acetate, bcip ADDITIVE, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 23, 2005 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.17→47.57 Å / Num. obs: 40016 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 11.19 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.059 / Net I/σ(I): 22.19
Reflection shellResolution: 1.17→1.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2882 / Rsym value: 0.526 / % possible all: 99.19

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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: structure of homolog from infectious bronchitis virus PDB:2BTL

2btl


Resolution: 1.17→47.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.123 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19132 2131 5.1 %RANDOM
Rwork0.16244 ---
all0.1638 40016 --
obs0.16389 40016 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: 11.191 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.05 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.054 Å0.041 Å
Luzzati d res low-6 Å
Luzzati sigma a0.244 Å0.221 Å
Refinement stepCycle: LAST / Resolution: 1.17→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 4 185 1289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211141
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9491560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65722.54555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6115176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2291511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02927
X-RAY DIFFRACTIONr_nbd_refined0.210.2506
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2792
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4790.219
X-RAY DIFFRACTIONr_mcbond_it1.1661.5702
X-RAY DIFFRACTIONr_mcangle_it1.7721127
X-RAY DIFFRACTIONr_scbond_it2.2863491
X-RAY DIFFRACTIONr_scangle_it3.2084.5433
X-RAY DIFFRACTIONr_rigid_bond_restr1.27131193
X-RAY DIFFRACTIONr_sphericity_free5.0873185
X-RAY DIFFRACTIONr_sphericity_bonded2.9531105
LS refinement shellResolution: 1.172→1.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 173 -
Rwork0.207 2882 -
obs--99.19 %

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