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- PDB-1ssk: Structure of the N-terminal RNA-binding Domain of the SARS CoV Nu... -

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Entry
Database: PDB / ID: 1ssk
TitleStructure of the N-terminal RNA-binding Domain of the SARS CoV Nucleocapsid Protein
ComponentsNucleocapsid proteinVirus
KeywordsSTRUCTURAL PROTEIN / nucleocapsid protein
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 / Attachment and Entry / SARS-CoV-1 targets host intracellular signalling and regulatory pathways ...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 / Attachment and Entry / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 activates/modulates innate immune responses / viral capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / host cell perinuclear region of cytoplasm / molecular adaptor activity / 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, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
Biological speciesSARS coronavirus
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsHuang, Q. / Yu, L. / Petros, A.M. / Gunasekera, A. / Liu, Z. / Xu, N. / Hajduk, P. / Mack, J. / Fesik, S.W. / Olejniczak, E.T.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of the N-Terminal RNA-Binding Domain of the SARS CoV Nucleocapsid Protein.
Authors: Huang, Q. / Yu, L. / Petros, A.M. / Gunasekera, A. / Liu, Z. / Xu, N. / Hajduk, P. / Mack, J. / Fesik, S.W. / Olejniczak, E.T.
History
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _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)17,1791
Polymers17,1791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

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


Mass: 17179.035 Da / Num. of mol.: 1 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: SARS / Gene: N / Plasmid: pet21d+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P59595

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131

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Sample preparation

DetailsContents: 0.5 mM N-terminal SARS CoV NP, U-15N,90% H2O/10% 2H2O, 50 mM sodium phosphate (pH 6.8) and 100 mM sodium chloride.
Sample conditionsIonic strength: 100mM Nacl / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR softwareName: CNS / Version: 2000 / Developer: brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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