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- PDB-7a6r: Structure of 14-3-3 gamma in complex with DAPK2 peptide containin... -

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Basic information

Entry
Database: PDB / ID: 7a6r
TitleStructure of 14-3-3 gamma in complex with DAPK2 peptide containing the 14-3-3 binding motif
Components
  • 14-3-3 protein gamma
  • DAPK2 C-terminal peptide
KeywordsSIGNALING PROTEIN / 14-3-3 protein / DAPK2 / kinase / complex / phosphorylation
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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting ...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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / 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 / 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 sequestering activity / AURKA Activation by TPX2 / protein kinase C binding / negative regulation of protein kinase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / 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 / intracellular protein localization / presynapse / regulation of protein localization / mitochondrial matrix / 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
14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 26, 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 / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5
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

Downloads & links

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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
E: DAPK2 C-terminal peptide
F: DAPK2 C-terminal peptide
G: DAPK2 C-terminal peptide
L: DAPK2 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)112,5268
Polymers112,5268
Non-polymers00
Water61334
1
A: 14-3-3 protein gamma
C: 14-3-3 protein gamma
E: DAPK2 C-terminal peptide
G: DAPK2 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)56,2634
Polymers56,2634
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-21 kcal/mol
Surface area22570 Å2
MethodPISA
2
B: 14-3-3 protein gamma
F: DAPK2 C-terminal peptide

D: 14-3-3 protein gamma
L: DAPK2 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)56,2634
Polymers56,2634
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x+y,-x,z+11
Buried area3760 Å2
ΔGint-20 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.620, 205.620, 74.091
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 54.08 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, MgCl2, PEG400, hexafluoro-2-propanol

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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: 2.7→30.64 Å / Num. obs: 31982 / % possible obs: 99.7 % / Redundancy: 4.39 % / Biso Wilson estimate: 47.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Net I/σ(I): 13.5
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3165 / CC1/2: 0.846 / Rrim(I) all: 0.539

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Processing

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

2b05


Resolution: 2.7→30.64 Å / SU ML: 0.4637 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 32.6063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 3015 4.94 %Random selection
Rwork0.2367 57964 --
obs0.2386 31982 95.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7375 0 0 34 7409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197480
X-RAY DIFFRACTIONf_angle_d0.403910128
X-RAY DIFFRACTIONf_chiral_restr0.03141154
X-RAY DIFFRACTIONf_plane_restr0.00281305
X-RAY DIFFRACTIONf_dihedral_angle_d16.4172762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.42791320.3912379X-RAY DIFFRACTION85.7
2.74-2.790.38251210.36032361X-RAY DIFFRACTION87.39
2.79-2.840.39581210.32132493X-RAY DIFFRACTION87.9
2.84-2.890.38441250.33412461X-RAY DIFFRACTION89.36
2.89-2.940.40491400.32192511X-RAY DIFFRACTION90.66
2.94-30.48161300.33382542X-RAY DIFFRACTION91.95
3-3.070.3971310.31462566X-RAY DIFFRACTION92.94
3.07-3.140.36811360.32892635X-RAY DIFFRACTION95.09
3.14-3.220.37111410.29582735X-RAY DIFFRACTION96.84
3.22-3.30.33151430.26942645X-RAY DIFFRACTION97.69
3.3-3.40.34291450.27912686X-RAY DIFFRACTION97.42
3.4-3.510.30561410.25682696X-RAY DIFFRACTION96.96
3.51-3.640.29951490.2332687X-RAY DIFFRACTION97.86
3.64-3.780.2581360.23822777X-RAY DIFFRACTION97.88
3.78-3.950.25831260.21322663X-RAY DIFFRACTION97.59
3.95-4.160.25411360.20472742X-RAY DIFFRACTION98.02
4.16-4.420.22881380.19622705X-RAY DIFFRACTION98.37
4.42-4.760.22891480.18942765X-RAY DIFFRACTION98.68
4.76-5.240.27861390.19752707X-RAY DIFFRACTION98.75
5.24-5.990.231400.23422742X-RAY DIFFRACTION99.17
5.99-7.520.20481470.20982762X-RAY DIFFRACTION99.08
7.53-30.640.1511500.15922704X-RAY DIFFRACTION97.87

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