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- PDB-6y4k: Crystal structure of human 14-3-3 gamma in complex with CaMKK2 14... -

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Basic information

Entry
Database: PDB / ID: 6y4k
TitleCrystal structure of human 14-3-3 gamma in complex with CaMKK2 14-3-3 binding motif Ser100 and Fusicoccin A
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 / Ca2+/calmodulin-dependent protein kinase / phosphorylation-dependent protein binding / positive regulation of cell-cell adhesion / 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 / Ca2+/calmodulin-dependent protein kinase / phosphorylation-dependent protein binding / positive regulation of cell-cell adhesion / 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 / regulation of signal transduction / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Activation of AMPK downstream of NMDARs / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / insulin-like growth factor receptor binding / protein sequestering activity / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / protein kinase C binding / calcium-mediated signaling / negative regulation of protein kinase activity / regulation of synaptic plasticity / receptor tyrosine kinase binding / cellular response to reactive oxygen species / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / positive regulation of T cell activation / protein localization / regulation of protein localization / presynapse / protein tyrosine kinase activity / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of protein phosphorylation / protein phosphorylation / 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 / membrane / cytosol / cytoplasm
Similarity search - Function
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. ...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
FUSICOCCIN / 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 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 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 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 1.2Nov 13, 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 gamma
B: 14-3-3 protein gamma
E: Calcium/calmodulin-dependent protein kinase kinase 2
F: Calcium/calmodulin-dependent protein kinase kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3045
Polymers56,6244
Non-polymers6811
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-38 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.852, 225.852, 72.963
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-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12
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: 4.74 Å3/Da / Density % sol: 74.07 %
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→48.62 Å / Num. obs: 22485 / % possible obs: 99.8 % / Redundancy: 21.83 % / Biso Wilson estimate: 90.16 Å2 / CC1/2: 1 / Rrim(I) all: 0.165 / Net I/σ(I): 18.91
Reflection shellResolution: 3→3.18 Å / Redundancy: 21.01 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 3562 / CC1/2: 0.495 / % possible all: 99.8

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Processing

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

2b05


Resolution: 3→17.08 Å / SU ML: 0.6033 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.875
RfactorNum. reflection% reflection
Rfree0.2921 1116 5 %
Rwork0.26 --
obs0.2616 22338 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 105.76 Å2
Refinement stepCycle: LAST / Resolution: 3→17.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 48 0 3530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283583
X-RAY DIFFRACTIONf_angle_d0.58944875
X-RAY DIFFRACTIONf_chiral_restr0.036571
X-RAY DIFFRACTIONf_plane_restr0.0037619
X-RAY DIFFRACTIONf_dihedral_angle_d21.73941258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.130.43271370.38842602X-RAY DIFFRACTION99.67
3.13-3.30.35141370.37412602X-RAY DIFFRACTION100
3.3-3.50.47051370.35432604X-RAY DIFFRACTION99.93
3.5-3.770.37881380.32792625X-RAY DIFFRACTION100
3.77-4.140.32551390.27812632X-RAY DIFFRACTION99.96
4.15-4.730.26081400.23612663X-RAY DIFFRACTION100
4.73-5.920.26881400.26032685X-RAY DIFFRACTION99.75
5.92-17.080.22671480.20342809X-RAY DIFFRACTION99.56

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