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- PDB-4zdr: Crystal structure of 14-3-3[zeta]-LKB1 fusion protein -

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Basic information

Entry
Database: PDB / ID: 4zdr
TitleCrystal structure of 14-3-3[zeta]-LKB1 fusion protein
Components14-3-3 protein zeta/delta,GGSGGS linker,Serine/threonine-protein kinase STK11
KeywordsPROTEIN BINDING / chimeric protein / regulatory protein / tumor suppressor / serine/threonine-protein kinase
Function / homology
Function and homology information


positive regulation of vesicle transport along microtubule / intracellular protein-containing complex / Golgi localization / LRR domain binding / AMPK inhibits chREBP transcriptional activation activity / Golgi reassembly / dendrite extension / negative regulation of epithelial cell proliferation involved in prostate gland development / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus ...positive regulation of vesicle transport along microtubule / intracellular protein-containing complex / Golgi localization / LRR domain binding / AMPK inhibits chREBP transcriptional activation activity / Golgi reassembly / dendrite extension / negative regulation of epithelial cell proliferation involved in prostate gland development / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / serine/threonine protein kinase complex / tissue homeostasis / establishment of Golgi localization / epithelial cell proliferation involved in prostate gland development / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / positive thymic T cell selection / Rap1 signalling / vasculature development / G1 to G0 transition / anoikis / negative regulation of cold-induced thermogenesis / regulation of Wnt signaling pathway / negative regulation of protein localization to nucleus / response to glucagon / KSRP (KHSRP) binds and destabilizes mRNA / FOXO-mediated transcription of cell death genes / response to ionizing radiation / GP1b-IX-V activation signalling / positive regulation of axonogenesis / regulation of dendrite morphogenesis / establishment of cell polarity / cellular response to UV-B / response to lipid / protein kinase activator activity / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of transforming growth factor beta receptor signaling pathway / activation of protein kinase activity / protein localization to nucleus / Regulation of localization of FOXO transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / 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 / positive regulation of autophagy / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / negative regulation of innate immune response / axonogenesis / protein dephosphorylation / regulation of ERK1 and ERK2 cascade / protein sequestering activity / response to activity / regulation of signal transduction by p53 class mediator / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / regulation of cell growth / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / peptidyl-threonine phosphorylation / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / Z disc / autophagy / positive regulation of protein localization to nucleus / melanosome / p53 binding / glucose homeostasis / T cell receptor signaling pathway / spermatogenesis / blood microparticle / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / vesicle / transmembrane transporter binding / protein autophosphorylation / regulation of cell cycle / non-specific serine/threonine protein kinase / cadherin binding / negative regulation of cell population proliferation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / mitochondrion / extracellular space
Similarity search - Function
Serine/Threonine kinase LKB1, catalytic 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 ...Serine/Threonine kinase LKB1, catalytic 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 / 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
PROPANE / 14-3-3 protein zeta/delta / Serine/threonine-protein kinase STK11
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsDing, S. / Shi, Z.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the 14-3-3 zeta-LKB1 fusion protein provides insight into a novel ligand-binding mode of 14-3-3.
Authors: Ding, S. / Zhou, R. / Zhu, Y.
History
DepositionApr 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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,GGSGGS linker,Serine/threonine-protein kinase STK11
B: 14-3-3 protein zeta/delta,GGSGGS linker,Serine/threonine-protein kinase STK11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,43213
Polymers60,6992
Non-polymers73311
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-21 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.262, 130.262, 264.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein 14-3-3 protein zeta/delta,GGSGGS linker,Serine/threonine-protein kinase STK11 / Protein kinase C inhibitor protein 1 / KCIP-1 / Liver kinase B1 / hLKB1 / Renal carcinoma antigen NY-REN-19


Mass: 30349.270 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230,UNP residues 333-340 / Mutation: T240E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: YWHAZ, STK11, LKB1, PJS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Codonplus / References: UniProt: P63104, UniProt: Q15831
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-TME / PROPANE / Propane


Mass: 44.096 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.4 M Li2SO4, 0.1 M BIS-TRIS propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 12, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.899→50 Å / Num. obs: 19507 / % possible obs: 100 % / Redundancy: 10.9 % / Net I/σ(I): 43
Reflection shellResolution: 2.899→2.95 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FJ3

4fj3


Resolution: 2.899→47.964 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 1951 10.01 %Random selection
Rwork0.1907 ---
obs0.1962 19496 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.899→47.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 46 8 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093782
X-RAY DIFFRACTIONf_angle_d1.195102
X-RAY DIFFRACTIONf_dihedral_angle_d15.2361365
X-RAY DIFFRACTIONf_chiral_restr0.044584
X-RAY DIFFRACTIONf_plane_restr0.004660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8989-2.97130.37091360.29911216X-RAY DIFFRACTION99
2.9713-3.05170.28561370.26411247X-RAY DIFFRACTION100
3.0517-3.14140.33241360.25981218X-RAY DIFFRACTION100
3.1414-3.24280.33641390.251253X-RAY DIFFRACTION100
3.2428-3.35870.32191380.24321234X-RAY DIFFRACTION100
3.3587-3.49310.27091370.2161235X-RAY DIFFRACTION100
3.4931-3.65210.2831390.20141244X-RAY DIFFRACTION100
3.6521-3.84450.24781400.18591262X-RAY DIFFRACTION100
3.8445-4.08530.24461390.1851244X-RAY DIFFRACTION100
4.0853-4.40050.22361380.16511243X-RAY DIFFRACTION100
4.4005-4.8430.22861400.15881277X-RAY DIFFRACTION100
4.843-5.54290.25091400.191255X-RAY DIFFRACTION100
5.5429-6.980.23331430.21621283X-RAY DIFFRACTION100
6.98-47.97030.20271490.16181334X-RAY DIFFRACTION99

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