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- PDB-7o07: 14-3-3sigma covalently bound to peptide (chloroacetamide-Cys inte... -

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Basic information

Entry
Database: PDB / ID: 7o07
Title14-3-3sigma covalently bound to peptide (chloroacetamide-Cys interaction)
Components
  • 14-3-3 protein sigma
  • Transcriptional coactivator YAP1
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / covalent peptide binding / protein/peptide interaction
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 / Activation of BAD and translocation to mitochondria ...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 / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / 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 / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSomsen, B.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)711.017.014 Netherlands
CitationJournal: Chem Sci / Year: 2021
Title: Covalent flexible peptide docking in Rosetta.
Authors: Tivon, B. / Gabizon, R. / Somsen, B.A. / Cossar, P.J. / Ottmann, C. / London, N.
History
DepositionMar 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 1, 2023Group: Advisory / Non-polymer description ...Advisory / Non-polymer description / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id
Revision 2.1Feb 7, 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
P: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9656
Polymers27,8682
Non-polymers974
Water5,693316
1
A: 14-3-3 protein sigma
P: Transcriptional coactivator YAP1
hetero molecules

A: 14-3-3 protein sigma
P: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93012
Polymers55,7354
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6317 Å2
ΔGint-62.3 kcal/mol
Surface area22863 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.592, 112.585, 63.212
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-303-

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: Initial 5 amino acids: GAMGS form the expression tag. The rest is the natural sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: P31947
#2: Protein/peptide Transcriptional coactivator YAP1


Mass: 1324.790 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: FCA in this case stand for phenylalanine chloroacetamide. This is a non-natural amino acid similar to a phenylalanine with a parasubsituted chloroacetamide for covalent binding to the 14-3-3 ...Details: FCA in this case stand for phenylalanine chloroacetamide. This is a non-natural amino acid similar to a phenylalanine with a parasubsituted chloroacetamide for covalent binding to the 14-3-3 protein (Cys38). Furthermore this peptide contains a C-terminal amide and a N-terminal acetyl group.
Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 316 / 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: 53.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.095 M HEPES (pH 7.3), 0.19 M CaCl2, 26% (v/v) PEG 400 and 5% (v/v) glycerol 12 mg/mL 14-3-3sdc; 1:1.2 molar equivalents 14-3-3:peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.2→66.6 Å / Num. obs: 92037 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shellResolution: 1.2→1.22 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4524 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
Aimlessdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N75

5n75


Resolution: 1.2→45.8802 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 8958 5.03 %
Rwork0.1836 169119 -
obs0.1842 91999 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.1 Å2 / Biso mean: 16.7039 Å2 / Biso min: 6.5 Å2
Refinement stepCycle: final / Resolution: 1.2→45.8802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 5 316 2225
Biso mean--16.97 27.33 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.2-1.21360.31942880.3385671
1.2136-1.22790.33493070.31165619
1.2279-1.24290.31663000.30935630
1.2429-1.25860.30673270.30015577
1.2586-1.27520.30452800.28375657
1.2752-1.29270.29322640.27735719
1.2927-1.31110.30843080.26585635
1.3111-1.33070.25282860.2555606
1.3307-1.35150.26343070.25765604
1.3515-1.37370.26243020.24655647
1.3737-1.39730.24592930.2365619
1.3973-1.42280.20973450.19145622
1.4228-1.45010.19062710.18425673
1.4501-1.47970.21053480.17695576
1.4797-1.51190.1863080.1745606
1.5119-1.54710.19083060.16935681
1.5471-1.58580.18662790.16365637
1.5858-1.62860.18813220.16795608
1.6286-1.67660.18172620.16575667
1.6766-1.73070.20072860.16355605
1.7307-1.79250.18962890.17225705
1.7925-1.86430.19873100.16885604
1.8643-1.94920.1923130.16955633
1.9492-2.05190.18862830.16745674
2.0519-2.18050.17712570.16285698
2.1805-2.34880.17473010.16045633
2.3488-2.58520.18233070.17075616
2.5852-2.95920.16113150.18235626
2.9592-3.7280.1842760.17265649
3.728-45.88010.17413180.16685622

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