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- PDB-7zit: 14-3-3 in complex with SARS-COV2 N phospho-peptide -

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Basic information

Entry
Database: PDB / ID: 7zit
Title14-3-3 in complex with SARS-COV2 N phospho-peptide
Components
  • 14-3-3 protein zeta/delta
  • Nucleoprotein
KeywordsPROTEIN BINDING / covid / coronavirus / N-phosphopeptide
Function / homology
Function and homology information


: / synaptic target recognition / Golgi reassembly / response to host immune response / NOTCH4 Activation and Transmission of Signal to the Nucleus / viral RNA genome packaging / establishment of Golgi localization / respiratory system process / negative regulation of interferon-beta production / tube formation ...: / synaptic target recognition / Golgi reassembly / response to host immune response / NOTCH4 Activation and Transmission of Signal to the Nucleus / viral RNA genome packaging / establishment of Golgi localization / respiratory system process / negative regulation of interferon-beta production / tube formation / regulation of synapse maturation / 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 / protein targeting / regulation of ERK1 and ERK2 cascade / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / Negative regulation of NOTCH4 signaling / molecular condensate scaffold activity / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / regulation of protein stability / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / melanosome / intracellular protein localization / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / angiogenesis / protein phosphatase binding / host cell Golgi apparatus / blood microparticle / vesicle / DNA-binding transcription factor binding / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / transmembrane transporter binding / Attachment and Entry / host cell perinuclear region of cytoplasm / protein phosphorylation / cadherin binding / ribonucleoprotein complex / protein domain specific binding / 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 domain ...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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / BENZOIC ACID / 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: 1.79 Å
AuthorsEisenreichova, A. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of Sciences61388963 Czech Republic
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Structural basis for SARS-CoV-2 nucleocapsid (N) protein recognition by 14-3-3 proteins.
Authors: Eisenreichova, A. / Boura, E.
History
DepositionApr 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: Nucleoprotein
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5638
Polymers54,2314
Non-polymers3324
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-23 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.180, 83.517, 111.356
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

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63104
#2: Protein/peptide Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 798.717 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 4 types, 398 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 9 0.2 M Sodium acetate 0.1 M Sodium cacodylate pH 6.5 30% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.79→30.32 Å / Num. obs: 62474 / % possible obs: 97.43 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.54 Å2 / Rmerge(I) obs: 0.03016 / Net I/σ(I): 21.6
Reflection shellResolution: 1.79→1.854 Å / Rmerge(I) obs: 0.4116 / Num. unique obs: 5637

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NAS

5nas


Resolution: 1.79→30.32 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2051 3121 5 %
Rwork0.1839 59334 -
obs0.1849 62455 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.83 Å2
Refinement stepCycle: LAST / Resolution: 1.79→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 23 394 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073827
X-RAY DIFFRACTIONf_angle_d0.88665149
X-RAY DIFFRACTIONf_chiral_restr0.0475571
X-RAY DIFFRACTIONf_plane_restr0.0079666
X-RAY DIFFRACTIONf_dihedral_angle_d11.0503528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.820.3271230.27082349X-RAY DIFFRACTION85.86
1.82-1.850.30181310.25462492X-RAY DIFFRACTION91.84
1.85-1.880.27921350.23522547X-RAY DIFFRACTION93.12
1.88-1.910.2231350.23682582X-RAY DIFFRACTION94.57
1.91-1.950.22961380.22752620X-RAY DIFFRACTION95.7
1.95-1.990.24821410.21842667X-RAY DIFFRACTION97.1
1.99-2.030.22881410.21832681X-RAY DIFFRACTION98.36
2.03-2.080.20791420.20842705X-RAY DIFFRACTION98.85
2.08-2.130.20751440.18952731X-RAY DIFFRACTION99.45
2.13-2.190.18421430.18412717X-RAY DIFFRACTION99.37
2.19-2.260.20041450.18562758X-RAY DIFFRACTION99.21
2.26-2.330.21091430.18162713X-RAY DIFFRACTION99.27
2.33-2.410.21341440.18682740X-RAY DIFFRACTION99.31
2.41-2.510.23971440.19272734X-RAY DIFFRACTION99.41
2.51-2.620.20351430.19472720X-RAY DIFFRACTION99.34
2.62-2.760.21671460.19692758X-RAY DIFFRACTION99.05
2.76-2.930.22241450.1942760X-RAY DIFFRACTION99.66
2.93-3.160.2161460.19442786X-RAY DIFFRACTION99.86
3.16-3.480.2241480.17632797X-RAY DIFFRACTION99.66
3.48-3.980.18271470.16882792X-RAY DIFFRACTION99.32
3.98-5.010.15261470.15032793X-RAY DIFFRACTION98.66
5.01-30.320.19841500.16692892X-RAY DIFFRACTION96.91

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