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- PDB-8r6e: SARS-CoV-2 Nucleocapsid dimerization domain -

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Basic information

Entry
Database: PDB / ID: 8r6e
TitleSARS-CoV-2 Nucleocapsid dimerization domain
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsFahoum, J. / Wiener, R. / Rouvinski, A. / Isupov, M.N.
Funding support Israel, 3items
OrganizationGrant numberCountry
Other privateThe Edmond and Benjamin de Rothschild Foundation
Israel Science Foundation338/19 Israel
Israel Ministry of Science and Technology2020000381 Israel
CitationJournal: To Be Published
Title: SARS-CoV-2 Nucleocapsid dimerization domain
Authors: Fahoum, J. / Wiener, R. / Rouvinski, A. / Isupov, M.N.
History
DepositionNov 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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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)27,20413
Polymers26,5202
Non-polymers68411
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-39 kcal/mol
Surface area12490 Å2
Unit cell
Length a, b, c (Å)43.620, 47.372, 134.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nucleoprotein


Mass: 13259.933 Da / Num. of mol.: 2
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: A0A7T7WQ79

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium chloride, 0.1M sodium/potassium phosphate 6.5 and 25% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.53→47.37 Å / Num. obs: 43189 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.997 / Net I/σ(I): 5.9
Reflection shellResolution: 1.53→1.55 Å / Num. unique obs: 1968 / CC1/2: 0.291

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→44.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.809 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26653 2104 4.9 %RANDOM
Rwork0.22475 ---
obs0.22671 40897 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.809 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å2-0 Å20 Å2
2--5.88 Å2-0 Å2
3----1.94 Å2
Refinement stepCycle: 1 / Resolution: 1.53→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 43 165 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122011
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161937
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.8472706
X-RAY DIFFRACTIONr_angle_other_deg0.5861.8034472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9725252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.817516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19610356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4143.509954
X-RAY DIFFRACTIONr_mcbond_other3.4033.508954
X-RAY DIFFRACTIONr_mcangle_it4.8216.2661194
X-RAY DIFFRACTIONr_mcangle_other4.8256.2651195
X-RAY DIFFRACTIONr_scbond_it4.4064.0161057
X-RAY DIFFRACTIONr_scbond_other4.4044.0171058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6237.071503
X-RAY DIFFRACTIONr_long_range_B_refined8.60337.122334
X-RAY DIFFRACTIONr_long_range_B_other8.60237.122334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 159 -
Rwork0.49 2973 -
obs--99.87 %

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