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- PDB-5oeg: Molecular tweezers modulate 14-3-3 protein-protein interactions -

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Basic information

Entry
Database: PDB / ID: 5oeg
TitleMolecular tweezers modulate 14-3-3 protein-protein interactions
Components14-3-3 protein sigma
KeywordsSIGNALING PROTEIN / 14-3-3 / Inhibition / Supramolecular ligand
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 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
Chem-9SZ / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å
AuthorsBier, D. / Ottmann, C.
CitationJournal: Nat Chem / Year: 2013
Title: Molecular tweezers modulate 14-3-3 protein-protein interactions.
Authors: Bier, D. / Rose, R. / Bravo-Rodriguez, K. / Bartel, M. / Ramirez-Anguita, J.M. / Dutt, S. / Wilch, C. / Klarner, F.G. / Sanchez-Garcia, E. / Schrader, T. / Ottmann, C.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionJul 26, 2017ID: 4HRU
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 2.0Apr 29, 2020Group: Atomic model / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.occupancy / _pdbx_struct_assembly.details ..._atom_site.occupancy / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.2Jan 17, 2024Group: Refinement description / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2483
Polymers26,4861
Non-polymers7622
Water2,342130
1
A: 14-3-3 protein sigma
hetero molecules

A: 14-3-3 protein sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4966
Polymers52,9722
Non-polymers1,5244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_456-x-1,y,-z+11
Buried area2360 Å2
ΔGint-31 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 154.710, 77.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

21A-521-

HOH

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Components

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


Mass: 26485.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AMGS - cleavage artifact / Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Chemical ChemComp-9SZ / (1R,5S,9S,16R,20R,24S,28S,35R)-3,22-Bis(dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaene


Mass: 726.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H32O8P2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M Tris/HCl, 10% PEG 8000, 500 mM MgCl2, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.15→19.58 Å / Num. obs: 6825 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.584 % / Biso Wilson estimate: 30.196 Å2 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.102 / Χ2: 0.926 / Net I/σ(I): 16.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
3.15-3.23.6410.2655.323060.312100
3.2-43.6370.1419.7531350.16699.9
4-53.6120.06519.3416280.07699.9
5-103.4980.0522.7915380.05999.8
10-123.2720.01851.71030.022100
12-19.583.0170.0247.451150.02473.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.15 Å19.58 Å
Translation3.15 Å19.58 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 3.15→19.58 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.844 / SU B: 18.689 / SU ML: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 342 5 %RANDOM
Rwork0.1811 ---
obs0.1852 6482 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.25 Å2 / Biso mean: 39.985 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å2-0 Å20 Å2
2---0.96 Å20 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 3.15→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 53 130 1958
Biso mean--51.97 23.53 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021884
X-RAY DIFFRACTIONr_bond_other_d0.0020.021717
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9832565
X-RAY DIFFRACTIONr_angle_other_deg1.0773.0053982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2235232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82324.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44215333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9711514
X-RAY DIFFRACTIONr_chiral_restr0.0630.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
LS refinement shellResolution: 3.15→3.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 25 -
Rwork0.237 467 -
all-492 -
obs--100 %

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