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- PDB-8bfc: Binary structure of 14-3-3s and RND3 phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 8bfc
TitleBinary structure of 14-3-3s and RND3 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Rho-related GTP-binding protein RhoE
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / phophopeptide
Function / homology
Function and homology information


RND3 GTPase cycle / small GTPase-mediated signal transduction / 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 ...RND3 GTPase cycle / small GTPase-mediated signal transduction / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / actin filament organization / 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 / cell migration / actin cytoskeleton organization / positive regulation of cell growth / cell adhesion / regulation of cell cycle / cadherin binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Rho-related GTP-binding protein RhoE / Small GTPase Rho / small GTPase Rho family profile. / 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 ...Rho-related GTP-binding protein RhoE / Small GTPase Rho / small GTPase Rho family profile. / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
14-3-3 protein sigma / Rho-related GTP-binding protein RhoE
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSomsen, B.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)711.017.014 Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Reversible Dual-Covalent Molecular Locking of the 14-3-3/ERR gamma Protein-Protein Interaction as a Molecular Glue Drug Discovery Approach.
Authors: Somsen, B.A. / Schellekens, R.J.C. / Verhoef, C.J.A. / Arkin, M.R. / Ottmann, C. / Cossar, P.J. / Brunsveld, L.
History
DepositionOct 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3667
Polymers28,2342
Non-polymers1335
Water5,152286
1
A: 14-3-3 protein sigma
B: Rho-related GTP-binding protein RhoE
hetero molecules

A: 14-3-3 protein sigma
B: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,73314
Polymers56,4684
Non-polymers26510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4810 Å2
ΔGint-91 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.366, 112.395, 62.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26553.875 Da / Num. of mol.: 1 / Mutation: C38N
Source method: isolated from a genetically manipulated source
Details: GAMGS at the beginning (-5 to -1) are part of the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Rho-related GTP-binding protein RhoE / Protein MemB / Rho family GTPase 3 / Rho-related GTP-binding protein Rho8 / Rnd3


Mass: 1679.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61587
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.1, 0.19 M CaCl2, 25% PEG400, 5% glycerol

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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 EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→45.59 Å / Num. obs: 57311 / % possible obs: 99.7 % / Redundancy: 5.3 % / CC1/2: 0.996 / Net I/σ(I): 15.2
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2675 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y1d
Resolution: 1.4→45.59 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 5483 4.98 %
Rwork0.1639 104584 -
obs0.1644 57289 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.83 Å2 / Biso mean: 16.155 Å2 / Biso min: 4.87 Å2
Refinement stepCycle: final / Resolution: 1.4→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 5 286 2166
Biso mean--17.55 25.96 -
Num. residues----242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.31181650.29323179334491
1.42-1.430.25231550.232634873642100
1.43-1.450.23091590.204135493708100
1.45-1.470.21592040.185834563660100
1.47-1.490.18832100.174135063716100
1.49-1.510.1962120.16734503662100
1.51-1.530.21031710.162435123683100
1.53-1.550.1981440.162135323676100
1.55-1.580.17511940.160834873681100
1.58-1.60.16922040.15583449365399
1.6-1.630.1751750.15393466364199
1.63-1.660.18781600.15553557371799
1.66-1.690.18091930.152434803673100
1.69-1.730.16451660.162835123678100
1.73-1.760.18732270.16834573684100
1.76-1.80.26351670.179935223689100
1.81-1.850.23841600.172135143674100
1.85-1.90.16342210.168834743695100
1.9-1.960.16961760.1635313707100
1.96-2.020.17551940.161834743668100
2.02-2.090.16221630.152235253688100
2.09-2.180.16991820.15433527370999
2.18-2.270.16941810.14813426360799
2.27-2.390.16041830.156835193702100
2.39-2.540.16361660.163235083674100
2.54-2.740.18322170.171634873704100
2.74-3.020.16331710.176235223693100
3.02-3.450.17392140.165134493663100
3.45-4.350.13212080.14733480368899
4.35-45.590.14431410.162135473688100

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