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- PDB-6eww: Structure of 14-3-3 zeta in complex with CaMKK2 14-3-3 binding motif -

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Basic information

Entry
Database: PDB / ID: 6eww
TitleStructure of 14-3-3 zeta in complex with CaMKK2 14-3-3 binding motif
Components
  • 14-3-3 protein zeta/delta
  • ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG
KeywordsSIGNALING PROTEIN / 14-3-3 protein / calcium/calmodulin-dependent protein kinase kinase 2 / CaMKK2 / phosphorylation
Function / homology
Function and homology information


regulation of protein kinase activity / synaptic target recognition / Golgi reassembly / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / regulation of synapse maturation ...regulation of protein kinase activity / synaptic target recognition / Golgi reassembly / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / regulation of synapse maturation / tube formation / Rap1 signalling / calcium/calmodulin-dependent protein kinase activity / negative regulation of protein localization to nucleus / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / KSRP (KHSRP) binds and destabilizes mRNA / Activation of RAC1 downstream of NMDARs / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of ERK1 and ERK2 cascade / 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 / negative regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to reactive oxygen species / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / calcium-mediated signaling / Negative regulation of NOTCH4 signaling / regulation of protein stability / MAPK cascade / intracellular protein localization / melanosome / positive regulation of protein phosphorylation / protein autophosphorylation / protein tyrosine kinase activity / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / transmembrane transporter binding / calmodulin binding / neuron projection / protein phosphorylation / cadherin binding / protein domain specific binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ubiquitin protein ligase binding / calcium ion binding / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / 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 zeta/delta / Calcium/calmodulin-dependent protein kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.679 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
DepositionNov 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: 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 1.4Jan 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
C: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
E: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG
F: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG
G: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG
H: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG


Theoretical massNumber of molelcules
Total (without water)110,4978
Polymers110,4978
Non-polymers00
Water2,054114
1
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
E: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG
F: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG


Theoretical massNumber of molelcules
Total (without water)55,2484
Polymers55,2484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-22 kcal/mol
Surface area21430 Å2
MethodPISA
2
C: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
G: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG
H: ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG


Theoretical massNumber of molelcules
Total (without water)55,2484
Polymers55,2484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-31 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.947, 60.309, 262.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26511.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63104
#2: Protein/peptide
ARG-LYS-LEU-SEP-LEU-GLN-GLU-ARG


Mass: 1112.198 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96RR4*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: PEG 2000, TRIS-HCl, HEPES, magnesium chloride, sodium fluoride, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.679→47.89 Å / Num. obs: 26274 / % possible obs: 99.7 % / Redundancy: 6.42 % / CC1/2: 0.998 / Rrim(I) all: 0.08 / Net I/σ(I): 17.37
Reflection shellResolution: 2.679→2.84 Å / Redundancy: 6.23 % / Mean I/σ(I) obs: 5.21 / Num. unique obs: 4126 / CC1/2: 0.956 / Rrim(I) all: 0.3 / % possible all: 98.9

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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: 4FJ3

4fj3


Resolution: 2.679→47.712 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / Phase error: 22.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1314 5 %Random selection
Rwork0.2078 ---
obs0.2091 26268 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.679→47.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 0 114 7232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097207
X-RAY DIFFRACTIONf_angle_d0.9699723
X-RAY DIFFRACTIONf_dihedral_angle_d24.3572677
X-RAY DIFFRACTIONf_chiral_restr0.0431105
X-RAY DIFFRACTIONf_plane_restr0.0051251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6789-2.78620.30361400.26972667X-RAY DIFFRACTION98
2.7862-2.9130.24861440.24432722X-RAY DIFFRACTION100
2.913-3.06650.27131440.22282749X-RAY DIFFRACTION100
3.0665-3.25860.29251430.24332709X-RAY DIFFRACTION100
3.2586-3.51010.26221460.2222768X-RAY DIFFRACTION100
3.5101-3.86320.24031450.19752760X-RAY DIFFRACTION100
3.8632-4.42190.22841470.18632795X-RAY DIFFRACTION100
4.4219-5.56980.19461480.20172818X-RAY DIFFRACTION100
5.5698-47.71940.20261570.1892966X-RAY DIFFRACTION100

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