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- PDB-7ce0: Crystal structure of 2019-nCoV nucleocapsid C-terminal domain (CT... -

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Basic information

Entry
Database: PDB / ID: 7ce0
TitleCrystal structure of 2019-nCoV nucleocapsid C-terminal domain (CTD) protein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / COVID-19 / RNA binding / nucleocapsid / 2019-nCoV / dimerization
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / 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 ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / molecular condensate scaffold activity / protein sequestering activity / VEGFR2 mediated vascular permeability / 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 / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / 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 (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 speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPeng, Y. / Qi, J. / Song, H. / Gao, G.F.
CitationJournal: Embo J. / Year: 2020
Title: Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design.
Authors: Peng, Y. / Du, N. / Lei, Y. / Dorje, S. / Qi, J. / Luo, T. / Gao, G.F. / Song, H.
History
DepositionJun 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 10, 2021Group: Structure summary / Category: entity_name_com / Item: _entity_name_com.name
Revision 1.3Nov 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
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)53,2004
Polymers53,2004
Non-polymers00
Water13,331740
1
A: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,6002
Polymers26,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-32 kcal/mol
Surface area11720 Å2
MethodPISA
2
B: Nucleoprotein
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,6002
Polymers26,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-31 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.726, 50.310, 69.134
Angle α, β, γ (deg.)73.876, 89.940, 82.552
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 13299.925 Da / Num. of mol.: 4 / Fragment: CTD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 4M Potassium formate, 0.1M BIS-TRIS propane, pH 9.0, 2% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 103766 / % possible obs: 91.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.87 Å2 / CC1/2: 0.996 / Net I/σ(I): 30.265
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 3 % / Num. unique obs: 3864 / CC1/2: 0.808

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJR

2cjr


Resolution: 1.5→26.82 Å / SU ML: 0.1361 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.3659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 3952 4.87 %
Rwork0.1767 77178 -
obs0.1773 81130 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 0 740 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313628
X-RAY DIFFRACTIONf_angle_d0.65064902
X-RAY DIFFRACTIONf_chiral_restr0.0755502
X-RAY DIFFRACTIONf_plane_restr0.0061646
X-RAY DIFFRACTIONf_dihedral_angle_d26.62981366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.2825880.21391936X-RAY DIFFRACTION62.95
1.52-1.540.22341050.20852066X-RAY DIFFRACTION67.74
1.54-1.560.22331030.20582128X-RAY DIFFRACTION68.99
1.56-1.580.2121150.20542259X-RAY DIFFRACTION73.93
1.58-1.60.2091250.20042363X-RAY DIFFRACTION78.34
1.6-1.630.24181250.20572472X-RAY DIFFRACTION80.2
1.63-1.650.1991340.19722552X-RAY DIFFRACTION85.27
1.65-1.680.21131360.20042728X-RAY DIFFRACTION86.87
1.68-1.710.23761340.19962775X-RAY DIFFRACTION92.44
1.71-1.740.20371530.21712891X-RAY DIFFRACTION93.52
1.74-1.770.25261480.21362897X-RAY DIFFRACTION95.07
1.77-1.810.18041490.19992915X-RAY DIFFRACTION95.99
1.81-1.850.21711590.19342893X-RAY DIFFRACTION96.34
1.85-1.890.20931510.19022965X-RAY DIFFRACTION96.41
1.89-1.940.21591450.19372934X-RAY DIFFRACTION95.8
1.94-1.990.23491640.18812939X-RAY DIFFRACTION96.49
1.99-2.050.19011430.18052984X-RAY DIFFRACTION97.54
2.05-2.110.17541530.1732932X-RAY DIFFRACTION96.95
2.11-2.190.18561700.17542993X-RAY DIFFRACTION97.26
2.19-2.280.17291470.17542909X-RAY DIFFRACTION95.47
2.28-2.380.17631680.17892935X-RAY DIFFRACTION97.24
2.38-2.510.21571350.18663000X-RAY DIFFRACTION98.12
2.51-2.660.18841700.18272950X-RAY DIFFRACTION96.98
2.66-2.870.17661470.1852997X-RAY DIFFRACTION98.34
2.87-3.160.21661530.1723039X-RAY DIFFRACTION98.76
3.16-3.610.18561620.16712843X-RAY DIFFRACTION93.53
3.61-4.550.16261310.13862877X-RAY DIFFRACTION94.24
4.55-26.820.13461390.15073006X-RAY DIFFRACTION98.04
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71482250907-0.01994084046780.004773665789620.2378408661770.08274332040640.457825959969-0.01388791422060.04372507559580.0421532967744-0.006501205372530.003019574996780.01420962318550.002574895645570.00842972602564-0.007459097697960.08882228616150.0009924752832777.38753537229E-50.05572533616750.008578508370070.083188722629411.322026954728.012279605411.4631085018
20.6908450024580.0659871165198-0.07362716717310.2723207886990.04853142086790.448133229824-0.0208556502573-0.0420573046675-0.03453783468920.01086763902890.008780765072040.035258346514-0.0134945480281-0.0200035454152-0.001495263540320.0932791349980.000281428301384-0.001340680705720.07164074236620.005249480447940.0903561063056-4.1132894413251.2448190753-4.85359189242
30.409640275232-0.02412808913280.003822438045210.27292261887-0.02443945621050.580156256915-0.04403017079250.0805128507538-0.0337115049584-0.008708796896360.0162270007381-0.0290949026652-0.0005441145710850.0504856375895-0.00927425717320.0789502327106-0.007527707303910.001745333532190.0921464364644-0.006306260204260.08344288387087.0497082111351.3360897567-17.9200284097
40.4860210119750.01357928257420.0522697365570.1919826923560.03063341577280.488988141621-0.056048974314-0.09445772680960.0421784908230.006807165453840.0243355429632-0.01992075922860.005776464468230.0367541697323-0.01793941415630.08451373747660.00484707916249-0.00134529865680.0962119519332-0.004666377997110.090724468274222.517727064927.672033199224.4856009036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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