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- PDB-6y8e: 14-3-3 Sigma in complex with phosphorylated MLF1 peptide -

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Basic information

Entry
Database: PDB / ID: 6y8e
Title14-3-3 Sigma in complex with phosphorylated MLF1 peptide
Components
  • 14-3-3 protein sigma
  • ARG-SER-PHE-SEP-GLU-PRO-PHE-GLY
KeywordsPROTEIN BINDING / 14-3-3 / MLF1 / complex / protein / protein-protein interactions
Function / homology
Function and homology information


regulation of cell cycle G1/S phase transition / myeloid progenitor cell differentiation / 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 ...regulation of cell cycle G1/S phase transition / myeloid progenitor cell differentiation / 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 / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein kinase A signaling / 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 / ciliary basal body / regulation of signal transduction by p53 class mediator / 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 / cilium / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / cell cycle / protein domain specific binding / DNA-templated transcription / regulation of DNA-templated transcription / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / DNA binding / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Myeloid leukemia factor / Myelodysplasia-myeloid leukemia factor 1-interacting protein / 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
Similarity search - Domain/homology
14-3-3 protein sigma / Myeloid leukemia factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsBallone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675179 Netherlands
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes.
Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
History
DepositionMar 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: ARG-SER-PHE-SEP-GLU-PRO-PHE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3987
Polymers29,2332
Non-polymers1645
Water6,612367
1
A: 14-3-3 protein sigma
P: ARG-SER-PHE-SEP-GLU-PRO-PHE-GLY
hetero molecules

A: 14-3-3 protein sigma
P: ARG-SER-PHE-SEP-GLU-PRO-PHE-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,79514
Polymers58,4674
Non-polymers32810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4950 Å2
ΔGint-60 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.167, 112.045, 62.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-304-

MG

21A-743-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

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


Mass: 28226.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide ARG-SER-PHE-SEP-GLU-PRO-PHE-GLY


Mass: 1006.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P58340*PLUS

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Non-polymers , 4 types, 372 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 28% PEG400, 5% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.973 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.42→29.28 Å / Num. obs: 54757 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 43.2
Reflection shellResolution: 1.42→1.45 Å / Num. unique obs: 2720 / CC1/2: 0.942

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
REFMACV5.5refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.42→29.28 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.58
RfactorNum. reflection% reflection
Rfree0.2007 2695 4.92 %
Rwork0.1741 --
obs0.1754 54731 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 5 367 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051966
X-RAY DIFFRACTIONf_angle_d0.7542676
X-RAY DIFFRACTIONf_dihedral_angle_d8.0191155
X-RAY DIFFRACTIONf_chiral_restr0.06298
X-RAY DIFFRACTIONf_plane_restr0.005350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.44580.22691320.21162661X-RAY DIFFRACTION100
1.4458-1.47360.23371380.19752714X-RAY DIFFRACTION100
1.4736-1.50370.2221430.18682704X-RAY DIFFRACTION100
1.5037-1.53640.21751420.18292719X-RAY DIFFRACTION100
1.5364-1.57220.2071500.18172699X-RAY DIFFRACTION100
1.5722-1.61150.1851430.17932740X-RAY DIFFRACTION100
1.6115-1.6550.18931270.18262729X-RAY DIFFRACTION100
1.655-1.70370.22821570.17562678X-RAY DIFFRACTION100
1.7037-1.75870.20341470.18792718X-RAY DIFFRACTION100
1.7587-1.82160.21191510.18312715X-RAY DIFFRACTION100
1.8216-1.89450.20741420.18272723X-RAY DIFFRACTION100
1.8945-1.98070.22341670.18122716X-RAY DIFFRACTION100
1.9807-2.08510.18761200.1762752X-RAY DIFFRACTION100
2.0851-2.21570.18811380.16812740X-RAY DIFFRACTION100
2.2157-2.38670.23711410.16842756X-RAY DIFFRACTION100
2.3867-2.62670.20961600.17632743X-RAY DIFFRACTION100
2.6267-3.00650.19631260.17792796X-RAY DIFFRACTION100
3.0065-3.78660.18041320.1612804X-RAY DIFFRACTION100
3.7866-29.2840.18771390.17012929X-RAY DIFFRACTION100

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