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- PDB-7vbf: 1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocap... -

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Basic information

Entry
Database: PDB / ID: 7vbf
Title1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucleocapsid dimerization domain
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J.
CitationJournal: To Be Published
Title: 1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5
Authors: Zhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J.
History
DepositionAug 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,6002
Polymers26,6002
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-32 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.710, 65.130, 84.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 13299.925 Da / Num. of mol.: 2 / Fragment: dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.3→18.18 Å / Num. obs: 112547 / % possible obs: 99.1 % / Redundancy: 10.9 % / Biso Wilson estimate: 14.7732563873 Å2 / Rsym value: 0.052 / Net I/σ(I): 19.3
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.549 / Num. unique obs: 59926

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6wji

6wji


Resolution: 1.3→18.1470797751 Å / SU ML: 0.117028392159 / Cross valid method: FREE R-VALUE / σ(F): 1.35007904007 / Phase error: 19.5653290504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203905612905 3727 3.31150541552 %
Rwork0.184986097528 108820 -
obs0.185605509437 112547 97.619088922 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.1820368238 Å2
Refinement stepCycle: LAST / Resolution: 1.3→18.1470797751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 0 189 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005439251061141874
X-RAY DIFFRACTIONf_angle_d0.8391267171332532
X-RAY DIFFRACTIONf_chiral_restr0.0876800531223256
X-RAY DIFFRACTIONf_plane_restr0.00673305646938334
X-RAY DIFFRACTIONf_dihedral_angle_d17.0338207036696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31650.2883950258321030.2755770978263042X-RAY DIFFRACTION73.429838898
1.3165-1.33380.2937055252451100.270457830973380X-RAY DIFFRACTION81.7330210773
1.3338-1.3520.2604213885811240.2604213885813665X-RAY DIFFRACTION88.6315789474
1.352-1.37130.271580122921290.2465057112833908X-RAY DIFFRACTION94.809769845
1.3713-1.39180.2188341103881394072X-RAY DIFFRACTION98.2730455076
1.3918-1.41350.2483315022761420.2140379125194140X-RAY DIFFRACTION99.8600746269
1.4135-1.43670.2556202738611360.2119270918524073X-RAY DIFFRACTION99.881347888
1.4367-1.46150.2093566906161420.1986116342254168X-RAY DIFFRACTION99.9536178108
1.4615-1.4880.2018174765041420.1947949630974106X-RAY DIFFRACTION99.9529411765
1.488-1.51660.2274521325521420.1932214882694168X-RAY DIFFRACTION100
1.5166-1.54760.1974479574061400.1805192306734081X-RAY DIFFRACTION99.8580553584
1.5476-1.58120.2162052940041410.1836128418044151X-RAY DIFFRACTION99.9301513388
1.5812-1.6180.1954478541241460.1754444992444109X-RAY DIFFRACTION100
1.618-1.65840.2012633119171380.1826094155914091X-RAY DIFFRACTION100
1.6584-1.70320.1981248462371460.183363781754195X-RAY DIFFRACTION100
1.7032-1.75330.2012226736061450.1872907023274126X-RAY DIFFRACTION99.9531944769
1.7533-1.80980.1886640690731420.1854076732474093X-RAY DIFFRACTION99.9292118924
1.8098-1.87450.2061448515071460.1807804388164129X-RAY DIFFRACTION100
1.8745-1.94940.1673994830431414121X-RAY DIFFRACTION99.9062353493
1.9494-2.0380.1860977874351410.1829435485324117X-RAY DIFFRACTION100
2.038-2.14530.2179825759631480.1791471088854110X-RAY DIFFRACTION99.9061473487
2.1453-2.27950.1836388205191390.1808791533174142X-RAY DIFFRACTION99.953303759
2.2795-2.45510.2194412520961450.1923168777554134X-RAY DIFFRACTION100
2.4551-2.70150.208297330211410.1986906070694123X-RAY DIFFRACTION100
2.7015-3.09070.2510638044751440.1887911459654107X-RAY DIFFRACTION100
3.0907-3.88770.1639806944221400.1761511149154129X-RAY DIFFRACTION100
3.8877-18.140.1957190346641350.1625801731654140X-RAY DIFFRACTION99.8831775701

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