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- PDB-7qik: SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-... -

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Basic information

Entry
Database: PDB / ID: 7qik
TitleSARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma
Components
  • 14-3-3 protein sigma
  • SER-SER-ARG-ASN-SEP-THR-PRO-GLY
KeywordsPEPTIDE BINDING PROTEIN / phosphopeptide-binding / universal regulatory hub / protein-peptide complex / coronavirus protein fragment
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / 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
BROMIDE ION / DI(HYDROXYETHYL)ETHER / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsSluchanko, N.N. / Tugaeva, K.V. / Smith, J.L.R. / Antson, A.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10031 Russian Federation
CitationJournal: To Be Published
Title: SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma
Authors: Sluchanko, N.N. / Tugaeva, K.V. / Smith, J.L.R. / Antson, A.A.
History
DepositionDec 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: 14-3-3 protein sigma
B: 14-3-3 protein sigma
E: SER-SER-ARG-ASN-SEP-THR-PRO-GLY
F: SER-SER-ARG-ASN-SEP-THR-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,33715
Polymers54,2874
Non-polymers1,05011
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.438, 111.274, 115.17
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26257.600 Da / Num. of mol.: 2 / Fragment: UNP residues 1-231
Source method: isolated from a genetically manipulated source
Details: wild-type residues 75-77 are mutated to Ala to improve crystallization
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide SER-SER-ARG-ASN-SEP-THR-PRO-GLY


Mass: 885.795 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 5 types, 349 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaBr, 100 mM BisTris propane pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.01→57.6 Å / Num. obs: 39958 / % possible obs: 96.6 % / Redundancy: 10.5 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.01→2.12 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4740 / CC1/2: 0.767 / % possible all: 80.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LU2

5lu2


Resolution: 2.01→20.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.178 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 2050 -RANDOM
Rwork0.1998 ---
obs0.2011 39836 96.2 %-
Displacement parametersBiso mean: 47.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.9977 Å20 Å20 Å2
2--9.3995 Å20 Å2
3----10.3972 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.01→20.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 48 338 3986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083752HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.865077HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1349SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes633HARMONIC5
X-RAY DIFFRACTIONt_it3715HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion483SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3338SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion17.91
LS refinement shellResolution: 2.01→2.03 Å
RfactorNum. reflection% reflection
Rfree0.4164 34 -
Rwork0.3283 --
obs0.3321 797 63.88 %
Refinement TLS params.

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)
10.75670.3868-0.22642.7693-0.41580.3830.05690.0740.07760.0740.1024-0.0920.0776-0.092-0.1593-0.0322-0.0198-0.029-0.0758-0.02140.0092-16.9756-22.561213.5275
21.29910.2326-0.04712.18660.18050.1467-0.2151-0.1384-0.0098-0.13840.1601-0.0482-0.0098-0.04820.055-0.07370.0136-0.0043-0.0527-0.01740.016-10.091516.01589.5385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 231
2X-RAY DIFFRACTION1{ A|* }A301 - 304
3X-RAY DIFFRACTION2{ B|* }B0 - 231
4X-RAY DIFFRACTION2{ B|* }B301 - 304

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