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- PDB-7de1: Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal R... -

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Basic information

Entry
Database: PDB / ID: 7de1
TitleCrystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / nucleocapsid protein / RNA binding / C-terminal domain
Function / homology
Function and homology information


cytoplasmic capsid assembly / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...cytoplasmic capsid assembly / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NOD1/2 Signaling Pathway / MHC class I protein complex / Interleukin-1 signaling / RNA stem-loop binding / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
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
DI(HYDROXYETHYL)ETHER / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, S. / Kang, S.
CitationJournal: Front Chem / Year: 2020
Title: Structural Insight Into the SARS-CoV-2 Nucleocapsid Protein C-Terminal Domain Reveals a Novel Recognition Mechanism for Viral Transcriptional Regulatory Sequences.
Authors: Yang, M. / He, S. / Chen, X. / Huang, Z. / Zhou, Z. / Zhou, Z. / Chen, Q. / Chen, S. / Kang, S.
History
DepositionNov 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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 / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1195
Polymers25,8012
Non-polymers3183
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-24 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.214, 101.438, 59.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 12900.470 Da / Num. of mol.: 2 / Fragment: C-terminal RNA binding domain
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 9.3 / Details: 100 mM CHES (pH 9.3) , 40% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→18.79 Å / Num. obs: 19057 / % possible obs: 99.27 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0588 / Net I/σ(I): 18.58
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.2126 / Num. unique obs: 1805 / CC1/2: 0.921

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJR

2cjr


Resolution: 2→18.48 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 1903 10 %
Rwork0.1713 17124 -
obs0.1765 19027 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.81 Å2 / Biso mean: 16.9664 Å2 / Biso min: 5.67 Å2
Refinement stepCycle: final / Resolution: 2→18.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 51 241 2067
Biso mean--31.77 24.34 -
Num. residues----223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.27181270.18871150127796
2.05-2.110.23991320.18561179131199
2.11-2.170.1971350.16561212134799
2.17-2.240.23551330.175912041337100
2.24-2.320.23751360.177912141350100
2.32-2.410.24531350.159812241359100
2.41-2.520.23511350.177812151350100
2.52-2.650.23491350.183112111346100
2.65-2.820.28221350.184512221357100
2.82-3.030.20561370.185212261363100
3.03-3.340.231370.181412291366100
3.34-3.820.2131390.168712561395100
3.82-4.790.1981400.13812561396100
4.8-18.790.19211470.17181326147399

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