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- PDB-7zmw: 14-3-3s binding to non-natural peptide 2c -

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Basic information

Entry
Database: PDB / ID: 7zmw
Title14-3-3s binding to non-natural peptide 2c
Components
  • 14-3-3 protein sigma
  • non-natural peptide 1
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / non-natural peptide
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 cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / 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 / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / 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 domain / Delta-Endotoxin; domain 1 / 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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSomsen, B.A. / Craenmehr, F.W.B. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)711.017.014 Netherlands
CitationJournal: Chem Sci / Year: 2022
Title: Functional mapping of the 14-3-3 hub protein as a guide to design 14-3-3 molecular glues.
Authors: Somsen, B.A. / Craenmehr, F.W.B. / Liu, W.W. / Koops, A.A. / Pennings, M.A.M. / Visser, E.J. / Ottmann, C. / Cossar, P.J. / Brunsveld, L.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: 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: non-natural peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6144
Polymers27,5662
Non-polymers492
Water4,774265
1
A: 14-3-3 protein sigma
B: non-natural peptide 1
hetero molecules

A: 14-3-3 protein sigma
B: non-natural peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2298
Polymers55,1324
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4910 Å2
ΔGint-35 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.976, 111.609, 62.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

MG

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Components

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


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The initial GAMGS amino acids form the expression tag of the protein
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide non-natural peptide 1


Mass: 1022.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 95 mM HEPES pH 7.5, 0.19 M CaCl2, 5% glycerol and 28% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→33.03 Å / Num. obs: 48998 / % possible obs: 97.4 % / Redundancy: 6 % / CC1/2: 0.996 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 1415 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
Cootmodel building
DIALSdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jc3

4jc3


Resolution: 1.8→33.03 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 2488 5.08 %
Rwork0.1792 46510 -
obs0.1814 48998 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.51 Å2 / Biso mean: 14.4028 Å2 / Biso min: 0.08 Å2
Refinement stepCycle: final / Resolution: 1.8→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 128 265 2222
Biso mean--30.16 22.02 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.23951220.21052294241684
1.83-1.870.23781070.2212449255691
1.87-1.910.22631540.20732460261492
1.91-1.960.24321390.19472525266492
1.96-2.010.24071140.18952524263893
2.01-2.060.22911400.18092557269794
2.06-2.120.24041520.16822578273096
2.12-2.190.22871200.1682631275197
2.19-2.270.22271420.17482673281598
2.27-2.360.18841430.17552634277798
2.36-2.470.24931460.18672698284498
2.47-2.60.22471370.1852638277598
2.6-2.760.23411270.18572665279298
2.76-2.970.23211550.18142652280798
2.97-3.270.23341660.17042625279199
3.27-3.740.19991470.160727112858100
3.74-4.710.20131330.15492572270595
4.71-33.030.19741440.20032624276897

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