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- PDB-7n45: Solution NMR structure of the N-terminal globular domain of the e... -

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Basic information

Entry
Database: PDB / ID: 7n45
TitleSolution NMR structure of the N-terminal globular domain of the endemic HKU1 coronavirus nucleocapsid protein
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / Nucleocapsid / N-terminal domain / RNA binding domain
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
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 coronavirus HKU1
MethodSOLUTION NMR / distance geometry
AuthorsCaruso, I.P. / Marques, A.L. / Santana-Silva, M.C. / Almeida, F.C.L. / Amorim, G.C.
Funding support Brazil, 5items
OrganizationGrant numberCountry
Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ)255940 Brazil
Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ)239016 Brazil
Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ)239229 Brazil
Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ)248462 Brazil
Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ)34567 Brazil
CitationJournal: To Be Published
Title: Solution NMR structure of the N-terminal globular domain of the endemic HKU1 coronavirus nucleocapsid protein.
Authors: Caruso, I.P. / Marques, A.L. / Santana-Silva, M.C. / Almeida, F.C.L. / Amorim, G.C.
History
DepositionJun 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)15,4721
Polymers15,4721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 150000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 15471.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: U3NAH8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D HNCA
151isotropic23D HN(CA)CB
181isotropic23D CBCA(CO)NH
171isotropic23D HNCO
161isotropic23D HN(CA)CO
191isotropic23D (H)CCH-TOCSY (H)CCH
1111isotropic23D (H)CCH-TOCSY (H)CCH
1101isotropic23D 1H-13C NOESY aliphatic
1121isotropic23D 1H-13C NOESY aromatic
1131isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 250 uM [U-13C; U-15N] Nucleocapsid protein NTD, 50 mM sodium phosphate, 3 mM sodium azide, 3 mM EDTA, 50 mM sodium chloride, 500 uM PMSF, 95% H2O/5% D2O
Label: 15N-13C_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMNucleocapsid protein NTD[U-13C; U-15N]1
50 mMsodium phosphatenatural abundance1
3 mMsodium azidenatural abundance1
3 mMEDTAnatural abundance1
50 mMsodium chloridenatural abundance1
500 uMPMSFnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
RefinementMethod: distance geometry / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150000 / Conformers submitted total number: 19

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