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- PDB-6ejl: Structure of 14-3-3 zeta in complex with ASK1 14-3-3 binding motif -

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Basic information

Entry
Database: PDB / ID: 6ejl
TitleStructure of 14-3-3 zeta in complex with ASK1 14-3-3 binding motif
Components
  • 14-3-3 protein zeta/delta
  • Mitogen-activated protein kinase kinase kinase 5
KeywordsSIGNALING PROTEIN / 14-3-3 protein / ASK1 / Apoptosis signal-regulating kinase 1
Function / homology
Function and homology information


cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / Golgi reassembly / synaptic target recognition / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / Golgi reassembly / synaptic target recognition / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / JUN kinase kinase kinase activity / establishment of Golgi localization / tube formation / endothelial cell apoptotic process / Rap1 signalling / negative regulation of protein localization to nucleus / positive regulation of p38MAPK cascade / KSRP (KHSRP) binds and destabilizes mRNA / intrinsic apoptotic signaling pathway in response to oxidative stress / GP1b-IX-V activation signalling / positive regulation of cardiac muscle cell apoptotic process / p38MAPK cascade / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / MAP kinase kinase kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Activation of BAD and translocation to mitochondria / positive regulation of protein kinase activity / positive regulation of myoblast differentiation / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / stress-activated MAPK cascade / positive regulation of JUN kinase activity / RHO GTPases activate PKNs / JNK cascade / negative regulation of TORC1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / protein sequestering activity / ERK1 and ERK2 cascade / cellular response to amino acid starvation / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / response to endoplasmic reticulum stress / regulation of ERK1 and ERK2 cascade / response to ischemia / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / apoptotic signaling pathway / positive regulation of JNK cascade / Negative regulation of NOTCH4 signaling / lung development / regulation of protein stability / cellular response to hydrogen peroxide / MAPK cascade / cellular senescence / melanosome / cellular response to tumor necrosis factor / protein phosphatase binding / angiogenesis / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / neuron apoptotic process / vesicle / transmembrane transporter binding / blood microparticle / protein kinase activity / cadherin binding / positive regulation of apoptotic process / protein domain specific binding / external side of plasma membrane / protein phosphorylation / innate immune response / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / protein homodimerization activity / protein-containing complex / RNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / 14-3-3 domain / Delta-Endotoxin; domain 1 ...MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / 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 / Sterile alpha motif/pointed domain superfamily / 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 / Mitogen-activated protein kinase kinase kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.382 Å
AuthorsPetrvalska, O. / Lentini Santo, D. / Obsilova, V. / Obsil, T.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European Commission675179 - TASPPI - H2020-MSCA-ITN-2015 Czech Republic
CitationJournal: To Be Published
Title: Crystal structure of 14-3-3 zeta in complex with ASK1 14-3-3 binding motif
Authors: Petrvalska, O. / Lentini Santo, D. / Obsilova, V. / Obsil, T.
History
DepositionSep 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Nov 6, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jan 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 zeta/delta
B: 14-3-3 protein zeta/delta
C: Mitogen-activated protein kinase kinase kinase 5
D: Mitogen-activated protein kinase kinase kinase 5


Theoretical massNumber of molelcules
Total (without water)55,0964
Polymers55,0964
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-34 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.980, 93.427, 68.491
Angle α, β, γ (deg.)90.00, 99.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

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Components

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


Mass: 26599.041 Da / Num. of mol.: 2
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 Mitogen-activated protein kinase kinase kinase 5 / Apoptosis signal-regulating kinase 1 / ASK-1 / MAPK/ERK kinase kinase 5 / MEKK 5


Mass: 949.020 Da / Num. of mol.: 2 / Fragment: UNP residues 963-970 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q99683, mitogen-activated protein kinase kinase kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Morpheus HT-96, condition H12

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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: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2.38→31.01 Å / Num. obs: 18601 / % possible obs: 99.4 % / Redundancy: 6.96 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.57
Reflection shellResolution: 2.38→2.53 Å / Redundancy: 6.89 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 7.15 / Num. unique obs: 2937 / CC1/2: 0.976 / % possible all: 97.8

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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: 1QJB

1qjb


Resolution: 2.382→30.322 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2154 928 5 %
Rwork0.1956 --
obs0.1966 18553 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.382→30.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 0 147 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083711
X-RAY DIFFRACTIONf_angle_d0.8945000
X-RAY DIFFRACTIONf_dihedral_angle_d25.0611404
X-RAY DIFFRACTIONf_chiral_restr0.042565
X-RAY DIFFRACTIONf_plane_restr0.005639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3822-2.50770.27321300.22472463X-RAY DIFFRACTION98
2.5077-2.66470.25331310.2342490X-RAY DIFFRACTION100
2.6647-2.87030.26771330.23412539X-RAY DIFFRACTION100
2.8703-3.15890.27221330.22582519X-RAY DIFFRACTION100
3.1589-3.61540.21071330.19362517X-RAY DIFFRACTION100
3.6154-4.55250.16551330.15982535X-RAY DIFFRACTION100
4.5525-30.32460.19191350.18022562X-RAY DIFFRACTION99

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