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- PDB-7zmu: 14-3-3s binding to non-natural peptide 2d -

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Basic information

Entry
Database: PDB / ID: 7zmu
Title14-3-3s binding to non-natural peptide 2d
Components
  • 14-3-3 protein sigma
  • non-natural peptide 2
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 protein kinase activity / 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 / protein export from nucleus / negative regulation of innate immune response / 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 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / 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 / cytoplasm / cytosol
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_3
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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4604
Polymers27,4122
Non-polymers492
Water4,558253
1
A: 14-3-3 protein sigma
B: non-natural peptide 2
hetero molecules

A: 14-3-3 protein sigma
B: non-natural peptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9218
Polymers54,8234
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4850 Å2
ΔGint-30 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.278, 112.007, 62.680
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

21A-571-

HOH

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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 2


Mass: 868.785 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.: 253 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 95 mM HEPES pH 7.1, 0.19 M CaCl2, 5% glycerol and 27% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→45.55 Å / Num. obs: 73822 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.988 / Net I/σ(I): 8.2
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1880 / CC1/2: 0.917

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Processing

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

4jc3


Resolution: 1.6→45.55 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 3757 5.09 %
Rwork0.2536 70064 -
obs0.2557 73821 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.32 Å2 / Biso mean: 18.1848 Å2 / Biso min: 4.24 Å2
Refinement stepCycle: final / Resolution: 1.6→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 109 253 2203
Biso mean--24.25 25.96 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.620.34461670.273325752742
1.62-1.640.34791180.271726332751
1.64-1.660.34051660.263525372703
1.66-1.690.32321500.245225782728
1.69-1.710.33361330.239226162749
1.71-1.740.25891320.242226232755
1.74-1.770.29931230.249825962719
1.77-1.80.29521270.24225952722
1.8-1.830.38271570.24926082765
1.83-1.870.29981150.268525932708
1.87-1.90.30251390.257125892728
1.9-1.950.35891510.270925922743
1.95-1.990.31611280.273426082736
1.99-2.040.37281360.2725802716
2.04-2.10.27011250.260326142739
2.1-2.160.34131440.253926022746
2.16-2.230.33291350.245526002735
2.23-2.310.24381340.253325892723
2.31-2.40.31651570.240225982755
2.4-2.510.24831330.256425782711
2.51-2.640.2751220.25425802702
2.64-2.810.33811440.268126142758
2.81-3.020.29141450.250726052750
3.02-3.330.28871760.249625742750
3.33-3.810.26741290.239825742703
3.81-4.80.24831340.242125942728
4.8-45.550.2351370.266526192756

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