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- PDB-7vbe: 1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocap... -

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Basic information

Entry
Database: PDB / ID: 7vbe
Title1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucleocapsid dimerization domain
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: 1.59 Å
AuthorsZhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J.
CitationJournal: To Be Published
Title: 1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0
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

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)24,5102
Polymers24,5102
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-34 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.330, 43.490, 59.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
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 / NC / Protein N


Mass: 12254.785 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 / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Polyethylene glycol monomethyl ether 550

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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 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.59→29.7825309017 Å / Num. obs: 69247 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 22.8399849791 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.4
Reflection shellResolution: 1.59→1.63 Å / Num. unique obs: 36711 / Rpim(I) all: 1.476

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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: 1.59→29.78 Å / SU ML: 0.237405355877 / Cross valid method: FREE R-VALUE / σ(F): 1.34350836859 / Phase error: 25.3021687535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.226384512698 3751 5.41684116279 %
Rwork0.203032927498 65496 -
obs0.204343912978 69247 99.7349886938 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.7181691242 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 143 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006246513403321712
X-RAY DIFFRACTIONf_angle_d0.8170740940242325
X-RAY DIFFRACTIONf_chiral_restr0.0557608435176244
X-RAY DIFFRACTIONf_plane_restr0.00699892215743308
X-RAY DIFFRACTIONf_dihedral_angle_d14.25947176321004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.61010.3819907434281380.3632937398542435X-RAY DIFFRACTION98.8854727133
1.6101-1.63130.3182224352021412382X-RAY DIFFRACTION99.4873817035
1.6313-1.65370.4000934732651390.3400267343642420X-RAY DIFFRACTION99.8049921997
1.6537-1.67730.3538830417941430.3338340105292471X-RAY DIFFRACTION99.9617590822
1.6773-1.70230.3472882971141320.3241747275542391X-RAY DIFFRACTION99.7627520759
1.7023-1.72890.3145774282751440.3009595066382446X-RAY DIFFRACTION99.8457979954
1.7289-1.75730.319361976191370.2847384651642428X-RAY DIFFRACTION99.844297392
1.7573-1.78750.2509272994791342425X-RAY DIFFRACTION99.7660818713
1.7875-1.820.2678768770361402421X-RAY DIFFRACTION99.5336183443
1.82-1.85510.3428922862381430.2694116840672408X-RAY DIFFRACTION99.5317986734
1.8551-1.89290.2676592597921440.2568954702922471X-RAY DIFFRACTION99.8854087089
1.8929-1.93410.280906455941400.2374375456322384X-RAY DIFFRACTION99.7628458498
1.9341-1.9790.2846413276021400.2327878781442444X-RAY DIFFRACTION99.5377503852
1.979-2.02850.2293331158551400.2223790025282386X-RAY DIFFRACTION99.9208860759
2.0285-2.08340.2311090909331420.2159522647782436X-RAY DIFFRACTION99.8450813323
2.0834-2.14460.2228361848821400.2174583039342439X-RAY DIFFRACTION99.8451413086
2.1446-2.21380.2389529981371380.2031239289432421X-RAY DIFFRACTION99.8829039813
2.2138-2.29290.2560369760331390.1970879752832465X-RAY DIFFRACTION99.9232540292
2.2929-2.38470.227417066441400.1920693666492413X-RAY DIFFRACTION100
2.3847-2.49320.2259111259171370.2068358592912405X-RAY DIFFRACTION100
2.4932-2.62460.2569717848271350.1973274821482438X-RAY DIFFRACTION100
2.6246-2.78890.2303848713191390.2017667421152424X-RAY DIFFRACTION100
2.7889-3.0040.2050236542971420.190087711382434X-RAY DIFFRACTION99.72899729
3.004-3.3060.2221475756941360.1891611535182444X-RAY DIFFRACTION100
3.306-3.78360.2008123575231340.1847264787922424X-RAY DIFFRACTION100
3.7836-4.76370.165860844821330.1509237195922451X-RAY DIFFRACTION100
4.7637-29.780.1893581422931410.1678892597562390X-RAY DIFFRACTION98.4059097978

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