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- PDB-9uj2: 14-3-3 zeta chimera with the S202R peptide of SARS-CoV-2 N (resid... -

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Basic information

Entry
Database: PDB / ID: 9uj2
Title14-3-3 zeta chimera with the S202R peptide of SARS-CoV-2 N (residues 200-213)
Components(14-3-3 protein zeta/delta,Peptide from Nucleoprotein) x 2
KeywordsSIGNALING PROTEIN / phosphopeptide / coronavirus / chimera
Function / homology
Function and homology information


synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / response to host immune response / viral RNA genome packaging / respiratory system process / negative regulation of interferon-beta production / regulation of synapse maturation / tube formation ...synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / response to host immune response / viral RNA genome packaging / respiratory system process / negative regulation of interferon-beta production / regulation of synapse maturation / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / CD28 dependent PI3K/Akt signaling / Activation of BAD and translocation to mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of ERK1 and ERK2 cascade / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / molecular condensate scaffold activity / Negative regulation of NOTCH4 signaling / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / regulation of protein stability / 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 / intracellular protein localization / melanosome / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / transmembrane transporter binding / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / protein phosphorylation / cadherin binding / protein domain specific binding / ribonucleoprotein complex / focal adhesion / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / 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. / 14-3-3 proteins signature 2. ...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. / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Nucleoprotein / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBoyko, K.M. / Matyuta, I.O. / Minyaev, M.E. / Perfilova, K.V. / Sluchanko, N.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness.
Authors: Perfilova, K.V. / Matyuta, I.O. / Minyaev, M.E. / Boyko, K.M. / Cooley, R.B. / Sluchanko, N.N.
History
DepositionApr 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 14-3-3 protein zeta/delta,Peptide from Nucleoprotein
A: 14-3-3 protein zeta/delta,Peptide from Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,47925
Polymers55,7432
Non-polymers1,73623
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint36 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.555, 84.452, 139.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein zeta/delta,Peptide from Nucleoprotein / Protein kinase C inhibitor protein 1 / KCIP-1 / N / Nucleocapsid protein / NC / Protein N


Mass: 27855.271 Da / Num. of mol.: 1 / Mutation: S202R,S58A,E73A,K74A,K75A,K157A,K158A,E159A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: YWHAZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63104, UniProt: P0DTC9
#2: Protein 14-3-3 protein zeta/delta,Peptide from Nucleoprotein / Protein kinase C inhibitor protein 1 / KCIP-1 / N / Nucleocapsid protein / NC / Protein N


Mass: 27887.336 Da / Num. of mol.: 1 / Mutation: S202R,S58A,E73A,K74A,K75A,K157A,K158A,E159A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: YWHAZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63104, UniProt: P0DTC9
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 1.8M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 2% v/v Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→21.76 Å / Num. obs: 67049 / % possible obs: 99.7 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.035 / Rrim(I) all: 0.111 / Χ2: 0.96 / Net I/σ(I): 15 / Num. measured all: 676288
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 97.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.857 / Num. measured all: 23631 / Num. unique obs: 3849 / CC1/2: 0.725 / Rpim(I) all: 0.367 / Rrim(I) all: 0.935 / Χ2: 0.91 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.073 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23302 3233 4.8 %RANDOM
Rwork0.19484 ---
obs0.19667 63642 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.992 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--2.17 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 1.8→21.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 117 437 4335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124054
X-RAY DIFFRACTIONr_bond_other_d0.0040.0163911
X-RAY DIFFRACTIONr_angle_refined_deg2.0791.8465428
X-RAY DIFFRACTIONr_angle_other_deg0.9521.7679028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.672529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77510735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024794
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02914
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_it1.4371.2761989
X-RAY DIFFRACTIONr_mcbond_other1.4361.2771990
X-RAY DIFFRACTIONr_mcangle_it2.1622.292499
X-RAY DIFFRACTIONr_mcangle_other2.1622.2912500
X-RAY DIFFRACTIONr_scbond_it2.4371.5772065
X-RAY DIFFRACTIONr_scbond_other2.4371.5772066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6962.7242922
X-RAY DIFFRACTIONr_long_range_B_refined5.88215.284707
X-RAY DIFFRACTIONr_long_range_B_other5.76614.074566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 226 -
Rwork0.295 4530 -
obs--97.26 %
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)
11.80490.3740.63511.33870.30312.1028-0.06080.1020.2416-0.02860.0212-0.0799-0.087-0.05320.03970.01160.01930.01130.06410.06130.0857-25.1365.5-8.693
20.8335-0.3770.29311.8207-0.36761.8751-0.01550.0070.10490.14560.01170.0156-0.00480.01750.00380.02040.0119-0.00980.0653-0.03670.0447-3.999-4.37920.565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 246
2X-RAY DIFFRACTION1B301 - 308
3X-RAY DIFFRACTION2A2 - 246
4X-RAY DIFFRACTION2A301 - 315

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