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- PDB-5oeh: Molecular tweezers modulate 14-3-3 protein-protein interactions. -

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Basic information

Entry
Database: PDB / ID: 5oeh
TitleMolecular tweezers modulate 14-3-3 protein-protein interactions.
Components14-3-3 protein sigma
KeywordsSIGNALING PROTEIN / 14-3-3 Protein / Inhibition / supramolecular ligands
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 / 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
Chem-9SZ / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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: 4HQW
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._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 1.2Jan 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 1.3Jan 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)27,3974
Polymers26,5431
Non-polymers8543
Water1,67593
1
A: 14-3-3 protein sigma
hetero molecules

A: 14-3-3 protein sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7948
Polymers53,0862
Non-polymers1,7086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_456-x-1,y,-z+11
Buried area2800 Å2
ΔGint-34 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 157.400, 77.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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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: GAMGS - 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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 0.09 M HEPES sodium salt, 1.26 M Tri-Sodium Citrate, 10 % Glycerol, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.54 Å / Num. obs: 15745 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.199 % / Biso Wilson estimate: 58.097 Å2 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.059 / Χ2: 0.944 / Net I/σ(I): 22.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.35-2.49.630.4674.749420.493100
2.4-2.59.5530.3745.7516740.396100
2.5-2.69.4330.2727.5814250.288100
2.6-2.79.1870.2239.0912110.23799.9
2.7-2.88.8060.16710.9610830.178100
2.8-2.99.0320.13713.79060.145100
2.9-39.590.11816.628080.124100
3-49.2460.05729.3743670.06100
4-45.548.8210.03945.4833290.04299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.54 Å
Translation2.5 Å45.54 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: 2.35→45.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.835 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.226
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 788 5 %RANDOM
Rwork0.2018 ---
obs0.2048 14956 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.62 Å2 / Biso mean: 53.748 Å2 / Biso min: 36.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 2.35→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 59 93 1917
Biso mean--53.98 59.61 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021862
X-RAY DIFFRACTIONr_bond_other_d0.0010.021685
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9862535
X-RAY DIFFRACTIONr_angle_other_deg1.0863.0053907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9885230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77424.81581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76115319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6591511
X-RAY DIFFRACTIONr_chiral_restr0.060.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 57 -
Rwork0.254 1083 -
all-1140 -
obs--100 %

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