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- PDB-7a6y: Structure of 14-3-3 gamma in complex with DAPK2 peptide stabilize... -

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Basic information

Entry
Database: PDB / ID: 7a6y
TitleStructure of 14-3-3 gamma in complex with DAPK2 peptide stabilized by FC-A
Components
  • 14-3-3 protein gamma
  • DAPK2 C-terminal peptide
KeywordsSIGNALING PROTEIN / 14-3-3 protein / DAPK2 / kinase / complex / phosphorylation / fusicoccin
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / 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 ...positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / 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 / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / insulin-like growth factor receptor binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / protein sequestering 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 / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / regulation of synaptic plasticity / receptor tyrosine kinase binding / positive regulation of T cell activation / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / protein localization / presynapse / regulation of protein localization / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / nucleus / membrane / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FUSICOCCIN / 14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHorvath, M. / Obsilova, V. / Obsil, T.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic19-00121S Czech Republic
CitationJournal: Commun Biol / Year: 2021
Title: 14-3-3 proteins inactivate DAPK2 by promoting its dimerization and protecting key regulatory phosphosites.
Authors: Horvath, M. / Petrvalska, O. / Herman, P. / Obsilova, V. / Obsil, T.
History
DepositionAug 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
J: DAPK2 C-terminal peptide
K: DAPK2 C-terminal peptide
L: DAPK2 C-terminal peptide
M: DAPK2 C-terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,56911
Polymers112,5268
Non-polymers2,0423
Water2,720151
1
A: 14-3-3 protein gamma
C: 14-3-3 protein gamma
J: DAPK2 C-terminal peptide
L: DAPK2 C-terminal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6256
Polymers56,2634
Non-polymers1,3622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-43 kcal/mol
Surface area22280 Å2
MethodPISA
2
D: 14-3-3 protein gamma
M: DAPK2 C-terminal peptide
hetero molecules

B: 14-3-3 protein gamma
K: DAPK2 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)56,9445
Polymers56,2634
Non-polymers6811
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x+y,-x,z+11
Buried area4730 Å2
ΔGint-31 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.502, 205.502, 74.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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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
DAPK2 C-terminal peptide


Mass: 931.914 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H56O12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, MgCl2, PEG400, hexafluoro-2-propanol, FC-A

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.5→29.68 Å / Num. obs: 40349 / % possible obs: 99.64 % / Redundancy: 4.23 % / Biso Wilson estimate: 45.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.041 / Net I/σ(I): 26.4
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4042 / CC1/2: 0.916 / Rrim(I) all: 0.292 / % possible all: 99.65

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B05

2b05


Resolution: 2.5→29.68 Å / SU ML: 0.3185 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 30.9377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 3667 4.91 %Random selection
Rwork0.223 70980 --
obs0.2248 40349 92.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7284 0 144 151 7579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287537
X-RAY DIFFRACTIONf_angle_d0.536910212
X-RAY DIFFRACTIONf_chiral_restr0.0351173
X-RAY DIFFRACTIONf_plane_restr0.00271287
X-RAY DIFFRACTIONf_dihedral_angle_d6.95094573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.32571240.30952393X-RAY DIFFRACTION79.2
2.53-2.570.33751090.30132341X-RAY DIFFRACTION78.68
2.57-2.60.38981230.28282298X-RAY DIFFRACTION79.69
2.6-2.640.28581250.29392387X-RAY DIFFRACTION78.99
2.64-2.680.32741100.29912237X-RAY DIFFRACTION76.65
2.68-2.730.27521240.2882374X-RAY DIFFRACTION80.01
2.73-2.780.31091320.27232457X-RAY DIFFRACTION84.11
2.78-2.830.36091370.26722689X-RAY DIFFRACTION90.29
2.83-2.880.29011360.27622740X-RAY DIFFRACTION91.94
2.88-2.940.3231400.27442806X-RAY DIFFRACTION93.46
2.94-30.40961490.28062768X-RAY DIFFRACTION95.39
3-3.070.34261540.28452833X-RAY DIFFRACTION96.67
3.07-3.150.3651400.27242907X-RAY DIFFRACTION97.47
3.15-3.230.32671500.27652928X-RAY DIFFRACTION99.35
3.23-3.330.31991560.25112931X-RAY DIFFRACTION99.77
3.33-3.440.33281520.24392974X-RAY DIFFRACTION99.18
3.44-3.560.27261540.23242927X-RAY DIFFRACTION97.93
3.56-3.70.24061460.21962724X-RAY DIFFRACTION92.94
3.7-3.870.25031420.20452728X-RAY DIFFRACTION92.82
3.87-4.070.22321540.19522845X-RAY DIFFRACTION96.68
4.07-4.330.20061500.19663000X-RAY DIFFRACTION100
4.33-4.660.20511580.17742962X-RAY DIFFRACTION100
4.66-5.130.20321540.18262950X-RAY DIFFRACTION100
5.13-5.860.31361480.22892926X-RAY DIFFRACTION100
5.86-7.370.20221520.20412956X-RAY DIFFRACTION100
7.37-29.680.16991480.16132899X-RAY DIFFRACTION97.1

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