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- PDB-9f35: Co-crystal structure of 14-3-3sigma in complex with B-Raf pS365 p... -

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Basic information

Entry
Database: PDB / ID: 9f35
TitleCo-crystal structure of 14-3-3sigma in complex with B-Raf pS365 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Serine/threonine-protein kinase B-raf
KeywordsPEPTIDE BINDING PROTEIN / 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 / phosphoserine residue binding ...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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / 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 stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / protein sequestering activity / positive regulation of cell adhesion / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / stem cell proliferation / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / 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 / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, Q.
Funding supportEuropean Union, Netherlands, China, 3items
OrganizationGrant numberCountry
European Union (EU)101098234European Union
Netherlands Organisation for Scientific Research (NWO)VI.Veni.212.27 Netherlands
Other governmentCSC 201906050031 China
Citation
Journal: Chem Sci / Year: 2025
Title: Proximity-enhanced cysteine-histidine crosslinking for elucidating intrinsically disordered and other protein complexes.
Authors: Wu, Q. / van den Wildenberg, S.A.H. / Brzoskowski, J.C.R. / van den Oetelaar, M.C.M. / Verhoef, C.J.A. / Genet, S.A.A.M. / Ottmann, C. / Markvoort, A.J. / Brunsveld, L. / Cossar, P.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionApr 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
B: Serine/threonine-protein kinase B-raf


Theoretical massNumber of molelcules
Total (without water)27,8672
Polymers27,8672
Non-polymers00
Water3,657203
1
A: 14-3-3 protein sigma
B: Serine/threonine-protein kinase B-raf

A: 14-3-3 protein sigma
B: Serine/threonine-protein kinase B-raf


Theoretical massNumber of molelcules
Total (without water)55,7344
Polymers55,7344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4420 Å2
ΔGint-24 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.782, 115.252, 64.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-373-

HOH

31A-488-

HOH

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Components

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


Mass: 26558.914 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 Serine/threonine-protein kinase B-raf


Mass: 1308.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 28% PEG400, 0.2M Cacl2, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.299→57.63 Å / Num. obs: 14439 / % possible obs: 99.92 % / Observed criterion σ(I): 3.7 / Redundancy: 3.74 % / Biso Wilson estimate: 19.35 Å2 / CC1/2: 0.974 / Net I/σ(I): 3.7
Reflection shellResolution: 2.299→2.381 Å / Num. unique obs: 1417 / CC1/2: 0.946 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→57.63 Å / SU ML: 0.362 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.8325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2982 706 4.89 %
Rwork0.2083 13733 -
obs0.2127 14439 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→57.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 203 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321953
X-RAY DIFFRACTIONf_angle_d1.28112637
X-RAY DIFFRACTIONf_chiral_restr0.0488290
X-RAY DIFFRACTIONf_plane_restr0.0103347
X-RAY DIFFRACTIONf_dihedral_angle_d12.6024280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.38121390.3042696X-RAY DIFFRACTION99.82
2.48-2.730.31591420.24582691X-RAY DIFFRACTION99.96
2.73-3.120.33531340.23042744X-RAY DIFFRACTION100
3.12-3.930.29391490.1722731X-RAY DIFFRACTION100
3.93-57.630.24371420.1762871X-RAY DIFFRACTION99.83

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