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- PDB-6fel: Structure of 14-3-3 gamma in complex with CaMKK2 14-3-3 binding m... -

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Basic information

Entry
Database: PDB / ID: 6fel
TitleStructure of 14-3-3 gamma in complex with CaMKK2 14-3-3 binding motif Ser511
Components
  • 14-3-3 protein gamma
  • Calcium/calmodulin-dependent protein kinase kinase 2
KeywordsSIGNALING PROTEIN / 14-3-3 protein / calcium/calmodulin-dependent protein kinase kinase 2 / CaMKK2 / phosphorylation
Function / homology
Function and homology information


positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calmodulin-dependent protein kinase activity / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of neuron differentiation / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / protein kinase C inhibitor activity ...positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / calmodulin-dependent protein kinase activity / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of neuron differentiation / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / regulation of signal transduction / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of AMPK downstream of NMDARs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / negative regulation of TORC1 signaling / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / insulin-like growth factor receptor binding / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein sequestering activity / protein kinase C binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium-mediated signaling / TP53 Regulates Metabolic Genes / regulation of synaptic plasticity / negative regulation of protein kinase activity / 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 / presynapse / protein tyrosine kinase activity / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of protein phosphorylation / protein domain specific binding / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of DNA-templated transcription / signal transduction / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
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
14-3-3 protein gamma / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsLentini Santo, D. / Obsilova, V. / Obsil, T.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation16-02739S Czech Republic
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: 14-3-3 protein directly interacts with the kinase domain of calcium/calmodulin-dependent protein kinase kinase (CaMKK2).
Authors: Psenakova, K. / Petrvalska, O. / Kylarova, S. / Lentini Santo, D. / Kalabova, D. / Herman, P. / Obsilova, V. / Obsil, T.
History
DepositionJan 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.4Nov 6, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein gamma
C: 14-3-3 protein gamma
B: 14-3-3 protein gamma
D: 14-3-3 protein gamma
E: Calcium/calmodulin-dependent protein kinase kinase 2
F: Calcium/calmodulin-dependent protein kinase kinase 2
G: Calcium/calmodulin-dependent protein kinase kinase 2
H: Calcium/calmodulin-dependent protein kinase kinase 2


Theoretical massNumber of molelcules
Total (without water)112,3268
Polymers112,3268
Non-polymers00
Water63135
1
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


Theoretical massNumber of molelcules
Total (without water)56,1634
Polymers56,1634
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-30 kcal/mol
Surface area22150 Å2
MethodPISA
2
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
G: Calcium/calmodulin-dependent protein kinase kinase 2
H: Calcium/calmodulin-dependent protein kinase kinase 2


Theoretical massNumber of molelcules
Total (without water)56,1634
Polymers56,1634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-29 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.734, 115.734, 203.963
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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.: 4
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: 881.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 5.6
Details: sodium citrate, potassium sodium tartrate, and ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Aug 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2.84→26.82 Å / Num. obs: 22801 / % possible obs: 94.4 % / Redundancy: 10.85 % / CC1/2: 0.991 / Rrim(I) all: 0.26 / Net I/σ(I): 11.19
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 10.81 % / Mean I/σ(I) obs: 2.26 / Num. unique obs: 2424 / Rrim(I) all: 0.97 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B05

2b05


Resolution: 2.84→26.82 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 32.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 1132 4.97 %Random selection
Rwork0.2278 ---
obs0.2304 22759 94.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.84→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 0 35 7441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047513
X-RAY DIFFRACTIONf_angle_d0.5510144
X-RAY DIFFRACTIONf_dihedral_angle_d25.4152834
X-RAY DIFFRACTIONf_chiral_restr0.0341138
X-RAY DIFFRACTIONf_plane_restr0.0031302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8391-2.96810.40631470.3532885X-RAY DIFFRACTION100
2.9681-3.12440.33971500.26482835X-RAY DIFFRACTION100
3.1244-3.31980.34361500.25682866X-RAY DIFFRACTION100
3.3198-3.57560.35621260.25432372X-RAY DIFFRACTION83
3.5756-3.93440.29581110.24562129X-RAY DIFFRACTION75
3.9344-4.50140.2391470.19232856X-RAY DIFFRACTION100
4.5014-5.66250.26371500.19872848X-RAY DIFFRACTION100
5.6625-26.82110.19231510.19272836X-RAY DIFFRACTION99

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