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- PDB-7qip: SARS-CoV-2 Nucleocapsid phosphopeptide 201-210 bound to human 14-... -

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Basic information

Entry
Database: PDB / ID: 7qip
TitleSARS-CoV-2 Nucleocapsid phosphopeptide 201-210 bound to human 14-3-3 sigma
Components
  • 14-3-3 protein sigma
  • ARG-GLY-TPO-SER-PRO-ALA-ARG-MET
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
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: 2.65 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

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: ARG-GLY-TPO-SER-PRO-ALA-ARG-MET
D: ARG-GLY-TPO-SER-PRO-ALA-ARG-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8847
Polymers54,7774
Non-polymers1063
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-53 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.688, 99.688, 58.575
Angle α, β, γ (deg.)90, 90, 90
Int Tables number76
Space group name H-MP41

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin / CLU1


Mass: 26257.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide ARG-GLY-TPO-SER-PRO-ALA-ARG-MET


Mass: 1131.160 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M AmSO4, 100 mM BisTris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→70.45 Å / Num. obs: 16912 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.989 / Net I/σ(I): 4.8
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 818 / CC1/2: 0.353 / % possible all: 100

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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: 2.65→70.49 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.927 / SU Rfree Blow DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 799 -RANDOM
Rwork0.2299 ---
obs0.2317 16670 98.6 %-
Displacement parametersBiso mean: 75.22 Å2
Baniso -1Baniso -2Baniso -3
1--3.6399 Å20 Å20 Å2
2---3.6399 Å20 Å2
3---7.2797 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.65→70.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 3 115 3755
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087142HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9112828HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2180SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1157HARMONIC5
X-RAY DIFFRACTIONt_it3689HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5823SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion16.15
LS refinement shellResolution: 2.65→2.67 Å
RfactorNum. reflection% reflection
Rfree0.6043 15 -
Rwork0.482 --
obs0.4866 428 95.72 %
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)
14.43190.5677-0.52972.50620.35372.21590.0207-0.05240.0452-0.0524-0.1582-0.17340.0452-0.17340.1375-0.1410.01310.0468-0.18050.05280.0612-53.4713-4.73053.8205
23.85191.387-1.45513.8854-1.25832.72670.06670.1324-0.24460.13240.1112-0.0557-0.2446-0.0557-0.1779-0.1768-0.03080.0124-0.21750.01770.2177-30.266923.8966-4.2171
34.09864.29635.820816.6309-4.9248.0005-0.1098-0.0962-0.6928-0.09620.28360.2184-0.69280.2184-0.1738-0.2324-0.031-0.1780.07660.03370.2454-55.6158-2.3427-2.3937
40-0.8339-3.999815.66742.65956.38170.3547-0.0029-0.2258-0.00290.0237-0.7243-0.2258-0.7243-0.3784-0.2141-0.06080.11380.136-0.11010.3683-31.795320.934-10.5119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 231
2X-RAY DIFFRACTION2{ B|* }B-1 - 231
3X-RAY DIFFRACTION3{ C|* }C203 - 210
4X-RAY DIFFRACTION4{ D|* }D201 - 210

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