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- PDB-2jw8: Solution structure of stereo-array isotope labelled (SAIL) C-term... -

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Basic information

Entry
Database: PDB / ID: 2jw8
TitleSolution structure of stereo-array isotope labelled (SAIL) C-terminal dimerization domain of SARS coronavirus nucleocapsid protein
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / SAIL / SARS coronavirus nucleocapsid protein / nucleocapsid packaging / Cytoplasm / Golgi apparatus / Phosphorylation / RNA-binding / Viral nucleoprotein / Virion / STRUCTURAL 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 / 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 / viral nucleocapsid / host cell Golgi apparatus / 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 protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
Biological speciesHuman SARS coronavirus
MethodSOLUTION NMR / simulated annealing, TORSION ANGLE DYNAMICS
AuthorsTakeda, M. / Chang, C. / Ikeya, T. / Guntert, P. / Chang, Y. / Hsu, Y. / Huang, T. / Kainosho, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method
Authors: Takeda, M. / Chang, C.K. / Ikeya, T. / Chang, Y.H. / Hsu, Y.L. / Huang, T.H. / Kainosho, M.
History
DepositionOct 6, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)29,1192
Polymers29,1192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleocapsid protein / N protein / NC


Mass: 14559.401 Da / Num. of mol.: 2 / Fragment: UNP residues 248-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Production host: Cell-free synthesis (others) / References: UniProt: P59595

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D CBCA(CO)NH

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Sample preparation

DetailsContents: 0.5mM SAIL-C-terminal dimerization domain of SARS coronavirus nucleocapsid protein, 10mM sodium phosphate, 50mM NaCl, 1mM EDTA, 1mM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM
Component: SARS coronavirus nucleocapsid protein residues 248-365
Isotopic labeling: full SAIL isotope labeling
Sample conditionsIonic strength: 50 / pH: 6 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGoddardchemical shift assignment
CYANA2.2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, TORSION ANGLE DYNAMICS / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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