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- PDB-7wzo: Crystal structure of the SARS-CoV-2 nucleocapsid protein N-termin... -

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Basic information

Entry
Database: PDB / ID: 7wzo
TitleCrystal structure of the SARS-CoV-2 nucleocapsid protein N-terminal domain in complex with Ubl1
Components
  • Nucleoprotein
  • nsp3
KeywordsVIRAL PROTEIN / coronavirus / ribonucleoprotein / protein-protein interaction / complex.
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / RNA stem-loop binding ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / RNA stem-loop binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / viral genome replication / protein sequestering activity / molecular condensate scaffold activity / VEGFR2 mediated vascular permeability / methyltransferase activity / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / Interleukin-1 signaling / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / methylation / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / viral nucleocapsid / endonuclease activity / symbiont-mediated suppression of host gene expression / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Attachment and Entry / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / induction by virus of host autophagy / cysteine-type endopeptidase activity / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / proteolysis / RNA binding / zinc ion binding / extracellular region / membrane / identical protein binding / cytoplasm
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 / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus ...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 / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Coronavirus 3Ecto domain profile. / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Replicase polyprotein 1a / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsNi, X.C. / Zhou, R.J. / Lei, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0702004 China
CitationJournal: Commun Biol / Year: 2023
Title: Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2.
Authors: Ni, X. / Han, Y. / Zhou, R. / Zhou, Y. / Lei, J.
History
DepositionFeb 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: nsp3
C: nsp3


Theoretical massNumber of molelcules
Total (without water)40,0793
Polymers40,0793
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Ubl1 is dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint2 kcal/mol
Surface area20240 Å2
Unit cell
Length a, b, c (Å)69.537, 69.537, 269.253
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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


Mass: 14315.905 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Protein nsp3 / / Non-structural protein 3 / PL2-PRO / Papain-like proteinase / PL-PRO


Mass: 12881.404 Da / Num. of mol.: 2 / Fragment: ubiquitin-like domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 4.69 Å3/Da / Density % sol: 73.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium citrate, pH 5.0, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97581 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97581 Å / Relative weight: 1
ReflectionResolution: 2.64→20.02 Å / Num. obs: 23164 / % possible obs: 99.7 % / Redundancy: 18.7 % / Biso Wilson estimate: 70.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.049 / Net I/σ(I): 13.2
Reflection shellResolution: 2.64→2.77 Å / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3003 / CC1/2: 0.68 / Rpim(I) all: 0.429

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VNU

7vnu


Resolution: 2.64→20.02 Å / SU ML: 0.3805 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 1231 5.33 %
Rwork0.2143 21874 -
obs0.2161 23105 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73 Å2
Refinement stepCycle: LAST / Resolution: 2.64→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 0 118 2840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882795
X-RAY DIFFRACTIONf_angle_d1.08393807
X-RAY DIFFRACTIONf_chiral_restr0.0658422
X-RAY DIFFRACTIONf_plane_restr0.0067494
X-RAY DIFFRACTIONf_dihedral_angle_d19.6202376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.750.39731280.33932398X-RAY DIFFRACTION99.06
2.75-2.870.39921430.29712365X-RAY DIFFRACTION100
2.87-3.020.31961110.2972423X-RAY DIFFRACTION100
3.02-3.210.3211270.2832370X-RAY DIFFRACTION100
3.21-3.460.29771340.24432406X-RAY DIFFRACTION100
3.46-3.80.2271520.21542397X-RAY DIFFRACTION100
3.8-4.350.23221440.18932459X-RAY DIFFRACTION99.96
4.35-5.460.19631430.17182453X-RAY DIFFRACTION100
5.46-20.020.22811490.19812603X-RAY DIFFRACTION99.96

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