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- PDB-6y6b: Crystal structure of human 14-3-3 gamma in complex with CaMKK2 14... -

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Basic information

Entry
Database: PDB / ID: 6y6b
TitleCrystal structure of human 14-3-3 gamma in complex with CaMKK2 14-3-3 binding motif Ser100 and 16-OMe-Fusicoccin H
Components
  • 14-3-3 protein gamma
  • Calcium/calmodulin-dependent protein kinase kinase 2
KeywordsSIGNALING PROTEIN / 14-3-3 protein / complex / CaMKK / Fusicoccin
Function / homology
Function and homology information


regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / positive regulation of cell-cell adhesion / Ca2+/calmodulin-dependent protein kinase / phosphorylation-dependent protein binding / CAMKK-AMPK signaling cascade / positive regulation of T cell mediated immune response to tumor cell / calcium/calmodulin-dependent protein kinase activity / regulation of neuron differentiation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...regulation of protein kinase activity / positive regulation of autophagy of mitochondrion / positive regulation of cell-cell adhesion / Ca2+/calmodulin-dependent protein kinase / phosphorylation-dependent protein binding / CAMKK-AMPK signaling cascade / positive regulation of T cell mediated immune response to tumor cell / calcium/calmodulin-dependent protein kinase activity / regulation of neuron differentiation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / 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 / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / insulin-like growth factor receptor binding / negative regulation of TORC1 signaling / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein kinase C binding / protein sequestering activity / AURKA Activation by TPX2 / cellular response to reactive oxygen species / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium-mediated signaling / receptor tyrosine kinase binding / regulation of synaptic plasticity / positive regulation of T cell activation / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / presynapse / MAPK cascade / regulation of protein localization / protein autophosphorylation / protein tyrosine kinase activity / calmodulin binding / protein phosphorylation / neuron projection / mitochondrial matrix / protein domain specific binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / calcium ion binding / positive regulation of DNA-templated transcription / signal transduction / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 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 ...14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-OD8 / 14-3-3 protein gamma / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsLentini Santo, D. / Obsilova, V. / Obsil, T.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation19-00121S Czech Republic
European CommissionTASPPI project, Grant Agreement 675179 Czech Republic
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Stabilization of Protein-Protein Interactions between CaMKK2 and 14-3-3 by Fusicoccins.
Authors: Lentini Santo, D. / Petrvalska, O. / Obsilova, V. / Ottmann, C. / Obsil, T.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: Calcium/calmodulin-dependent protein kinase kinase 2
D: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1245
Polymers56,6244
Non-polymers5011
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-24 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.266, 226.266, 72.993
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein 14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27199.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61981
#2: Protein/peptide Calcium/calmodulin-dependent protein kinase kinase 2 / CaMKK 2 / Calcium/calmodulin-dependent protein kinase kinase beta / CaMKK beta


Mass: 1112.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase
#3: Chemical ChemComp-OD8 / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[[(1~{S},3~{R},6~{S},7~{S},8~{R},9~{R},10~{R},11~{R},14~{S})-14-(me thoxymethyl)-3,10-dimethyl-9-oxidanyl-6-propan-2-yl-8-tricyclo[9.3.0.0^{3,7}]tetradecanyl]oxy]oxane-3,4,5-triol / 16-OMe-Fusicoccin H


Mass: 500.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H48O8
Has ligand of interestN
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: 4.76 Å3/Da / Density % sol: 74.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG400, HEPES, magnesium chloride, hexafluoropropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.08→48.99 Å / Num. obs: 20904 / % possible obs: 99.9 % / Redundancy: 21.72 % / Biso Wilson estimate: 110.21 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.28 / Net I/σ(I): 11.53
Reflection shellResolution: 3.08→3.26 Å / Redundancy: 22 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 3285 / CC1/2: 0.226 / Rrim(I) all: 4.97 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B05

2b05


Resolution: 3.08→17.75 Å / SU ML: 0.4663 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2818 1039 5.01 %
Rwork0.242 19713 -
obs0.244 20752 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.9 Å2
Refinement stepCycle: LAST / Resolution: 3.08→17.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 35 0 3669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013722
X-RAY DIFFRACTIONf_angle_d0.35695063
X-RAY DIFFRACTIONf_chiral_restr0.0295592
X-RAY DIFFRACTIONf_plane_restr0.002650
X-RAY DIFFRACTIONf_dihedral_angle_d8.6452528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.240.42761450.39952746X-RAY DIFFRACTION99.69
3.24-3.440.44541460.36982766X-RAY DIFFRACTION99.86
3.44-3.710.33591460.31222776X-RAY DIFFRACTION100
3.71-4.070.30321470.26732788X-RAY DIFFRACTION100
4.07-4.650.27561480.2262814X-RAY DIFFRACTION100
4.65-5.830.29131490.2382841X-RAY DIFFRACTION99.83
5.83-17.750.21471580.18992982X-RAY DIFFRACTION99.81

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