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- PDB-5nas: Crystal structure of human 14-3-3 zeta in complex with PI4KIIIB p... -

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Basic information

Entry
Database: PDB / ID: 5nas
TitleCrystal structure of human 14-3-3 zeta in complex with PI4KIIIB peptide
Components
  • 14-3-3 protein zeta/delta
  • Phosphatidylinositol 4-kinase beta
KeywordsTRANSFERASE / phosphoserine / kinase / regulation / phosphatidylinositol
Function / homology
Function and homology information


1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Golgi reassembly / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / phosphatidylinositol biosynthetic process / Rap1 signalling ...1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Golgi reassembly / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / phosphatidylinositol biosynthetic process / Rap1 signalling / phosphatidylinositol-mediated signaling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / lysosome organization / GP1b-IX-V activation signalling / inner ear development / phosphatidylinositol phosphate biosynthetic process / 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 / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / receptor-mediated endocytosis / negative regulation of innate immune response / protein sequestering activity / regulation of ERK1 and ERK2 cascade / 14-3-3 protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / melanosome / blood microparticle / DNA-binding transcription factor binding / vesicle / mitochondrial outer membrane / transmembrane transporter binding / endosome / cadherin binding / phosphorylation / Golgi membrane / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...: / PI4KB/PIK1, accessory (PIK) domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / 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 / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein zeta/delta / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsBoura, E. / Eisenreichova, A.
CitationJournal: To Be Published
Title: Crystal structure of human 14-3-3 zeta in complex with PI4KIIIB peptide
Authors: Boura, E. / Eisenreichova, A.
History
DepositionFeb 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: Phosphatidylinositol 4-kinase beta
D: Phosphatidylinositol 4-kinase beta


Theoretical massNumber of molelcules
Total (without water)55,0844
Polymers55,0844
Non-polymers00
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-25 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.822, 83.553, 111.538
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: 26444.891 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 Phosphatidylinositol 4-kinase beta / PtdIns 4-kinase beta / NPIK / PI4K92


Mass: 1097.182 Da / Num. of mol.: 2 / Fragment: UNP residues 289-297 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: MES, PEG, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.08→48.94 Å / Num. obs: 41025 / % possible obs: 99.99 % / Redundancy: 15.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09339 / Net I/σ(I): 21.76
Reflection shellResolution: 2.08→2.154 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.9849 / Mean I/σ(I) obs: 3.38 / Num. unique obs: 4034 / CC1/2: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHO

5lho
PDB Unreleased entry


Resolution: 2.08→48.94 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.02
RfactorNum. reflection% reflection
Rfree0.2311 2052 5 %
Rwork0.1879 --
obs0.19 41010 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 0 239 4029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083840
X-RAY DIFFRACTIONf_angle_d1.0235168
X-RAY DIFFRACTIONf_dihedral_angle_d14.091474
X-RAY DIFFRACTIONf_chiral_restr0.046574
X-RAY DIFFRACTIONf_plane_restr0.005668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.12840.32261350.26822553X-RAY DIFFRACTION100
2.1284-2.18160.32291350.2472569X-RAY DIFFRACTION100
2.1816-2.24060.28191340.22512557X-RAY DIFFRACTION100
2.2406-2.30650.23371350.20392562X-RAY DIFFRACTION100
2.3065-2.3810.2781360.20232570X-RAY DIFFRACTION100
2.381-2.46610.21191350.19452564X-RAY DIFFRACTION100
2.4661-2.56480.24941360.19742586X-RAY DIFFRACTION100
2.5648-2.68150.2691350.20772566X-RAY DIFFRACTION100
2.6815-2.82290.27591350.21422575X-RAY DIFFRACTION100
2.8229-2.99970.24171370.21252603X-RAY DIFFRACTION100
2.9997-3.23130.26381370.21372605X-RAY DIFFRACTION100
3.2313-3.55640.23441380.19822609X-RAY DIFFRACTION100
3.5564-4.07080.20841370.1812602X-RAY DIFFRACTION100
4.0708-5.12790.20741400.1522664X-RAY DIFFRACTION100
5.1279-48.95540.19721470.1642773X-RAY DIFFRACTION100

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