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- PDB-6y8a: 14-3-3 Sigma in complex with phosphorylated camkk2{pS511} peptide -

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Basic information

Entry
Database: PDB / ID: 6y8a
Title14-3-3 Sigma in complex with phosphorylated camkk2{pS511} peptide
Components
  • 14-3-3 protein sigma
  • Calcium/calmodulin-dependent protein kinase kinase 2
KeywordsPROTEIN BINDING / 14-3-3 / camkk2{pS511} / complex / protein / protein-protein interactions
Function / homology
Function and homology information


regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / regulation of epidermal cell division / protein kinase C inhibitor activity ...regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calcium/calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / 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 / Activation of AMPK downstream of NMDARs / 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 / cellular response to reactive oxygen species / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium-mediated signaling / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / MAPK cascade / regulation of protein localization / protein autophosphorylation / positive regulation of cell growth / protein tyrosine kinase activity / calmodulin binding / protein phosphorylation / regulation of cell cycle / neuron projection / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / Serine/threonine-protein kinase, active site ...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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
14-3-3 protein sigma / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2176
Polymers29,1082
Non-polymers1084
Water7,098394
1
A: 14-3-3 protein sigma
P: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules

A: 14-3-3 protein sigma
P: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,43312
Polymers58,2174
Non-polymers2178
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4720 Å2
ΔGint-73 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.243, 112.139, 62.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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-303-

MG

21A-766-

HOH

31A-780-

HOH

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Components

#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 Calcium/calmodulin-dependent protein kinase kinase 2 / CaMKK 2 / Calcium/calmodulin-dependent protein kinase kinase beta / CaMKK beta


Mass: 881.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / 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.: 394 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
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: 1.5→29.325 Å / Num. obs: 45770 / % possible obs: 96.5 % / Redundancy: 11.1 % / Biso Wilson estimate: 15.88 Å2 / CC1/2: 0.999 / Net I/σ(I): 26.5
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1763 / CC1/2: 0.87

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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: 1.5→29.325 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.2006 2286 5 %
Rwork0.1714 --
obs0.1729 45751 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 4 394 2244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052024
X-RAY DIFFRACTIONf_angle_d0.7582778
X-RAY DIFFRACTIONf_dihedral_angle_d6.0922028
X-RAY DIFFRACTIONf_chiral_restr0.042317
X-RAY DIFFRACTIONf_plane_restr0.005364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.53270.2472990.2112181X-RAY DIFFRACTION78
1.5327-1.56840.26441270.19552437X-RAY DIFFRACTION89
1.5684-1.60760.25881210.17912673X-RAY DIFFRACTION97
1.6076-1.6510.19811480.17692750X-RAY DIFFRACTION99
1.651-1.69960.17811310.17422747X-RAY DIFFRACTION100
1.6996-1.75450.22851540.17622744X-RAY DIFFRACTION100
1.7545-1.81720.22111330.18482752X-RAY DIFFRACTION100
1.8172-1.88990.24091560.17982757X-RAY DIFFRACTION100
1.8899-1.97590.20461520.18162756X-RAY DIFFRACTION100
1.9759-2.08010.20351790.17152730X-RAY DIFFRACTION100
2.0801-2.21030.19451500.16572768X-RAY DIFFRACTION100
2.2103-2.38090.19421520.16282767X-RAY DIFFRACTION100
2.3809-2.62040.19961420.17372809X-RAY DIFFRACTION100
2.6204-2.99920.21091390.17712821X-RAY DIFFRACTION100
2.9992-3.77750.17941540.15912816X-RAY DIFFRACTION100
3.7775-29.3250.19141490.16862957X-RAY DIFFRACTION100

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