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- PDB-5wxn: Structure of the LKB1 and 14-3-3 complex -

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Basic information

Entry
Database: PDB / ID: 5wxn
TitleStructure of the LKB1 and 14-3-3 complex
Components
  • 14-3-3 protein zeta/delta
  • Serine/threonine-protein kinase STK11
KeywordsPROTEIN BINDING/TRANSFERASE / Kinase / Tumor suppressor / Protein Complex / PROTEIN BINDING-TRANSFERASE complex
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
14-3-3 protein zeta/delta / Serine/threonine-protein kinase STK11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsDing, S. / Shi, Z.B.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure of the complex of phosphorylated liver kinase B1 and 14-3-3 zeta
Authors: Lu, Y. / Ding, S. / Zhou, R. / Wu, J.
History
DepositionJan 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
B: 14-3-3 protein zeta/delta
C: Serine/threonine-protein kinase STK11
D: Serine/threonine-protein kinase STK11


Theoretical massNumber of molelcules
Total (without water)64,3564
Polymers64,3564
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-33 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.771, 85.382, 112.738
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: 30444.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63104
#2: Protein/peptide Serine/threonine-protein kinase STK11


Mass: 1733.880 Da / Num. of mol.: 2 / Fragment: UNP residues 331-343 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15831
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.15 M ammonium chloride, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2015
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. obs: 15953 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 22.07
Reflection shellResolution: 2.93→2.98 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 1.78 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZDR

4zdr


Resolution: 2.93→44.563 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1559 10 %
Rwork0.1934 --
obs0.1997 15587 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.93→44.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 0 18 3650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093697
X-RAY DIFFRACTIONf_angle_d1.2395020
X-RAY DIFFRACTIONf_dihedral_angle_d6.8783017
X-RAY DIFFRACTIONf_chiral_restr0.066584
X-RAY DIFFRACTIONf_plane_restr0.008649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9301-3.02460.39751390.32081252X-RAY DIFFRACTION100
3.0246-3.13270.381390.28291253X-RAY DIFFRACTION100
3.1327-3.25810.33151400.23621254X-RAY DIFFRACTION100
3.2581-3.40630.31921390.2351258X-RAY DIFFRACTION100
3.4063-3.58590.33061390.22281244X-RAY DIFFRACTION99
3.5859-3.81040.26441420.19261277X-RAY DIFFRACTION100
3.8104-4.10440.22991420.16871273X-RAY DIFFRACTION100
4.1044-4.51710.25211430.1561276X-RAY DIFFRACTION100
4.5171-5.16990.22351420.151288X-RAY DIFFRACTION100
5.1699-6.51030.24731450.21091299X-RAY DIFFRACTION100
6.5103-44.56850.20251490.18591354X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.0876-4.81583.80713.6364-2.06875.56120.57840.20640.4978-1.0963-0.3988-0.5482-0.14120.6389-0.15660.811-0.18030.14630.9716-0.01840.567969.821396.2012-14.0374
23.60531.73812.48422.8330.40636.0598-0.3101-0.17150.1603-0.1023-0.22640.0869-0.8436-0.32670.50910.60330.11110.01130.7233-0.0990.420160.192791.22074.5511
35.55921.61013.46316.43310.50547.4845-0.5048-0.02950.2653-0.52170.14740.6667-1.2572-1.31960.2990.52920.1039-0.06330.80110.0890.518748.987689.9798-9.6709
46.8448-1.9620.38498.47751.80286.69160.02160.7134-0.4286-0.5974-0.2710.6314-0.2487-0.55160.24310.40620.003-0.03590.7362-0.04680.433750.678373.4574-11.0719
54.559-0.33890.33542.153-0.14574.4688-0.18470.24330.3858-0.03270.1321-0.433-0.44620.3171-0.02040.5508-0.11110.04370.6765-0.13580.574182.666993.46968.529
62.21120.05152.53736.98550.84233.049-0.1322-0.40260.27980.1978-0.014-0.87040.02240.47130.11930.4231-0.08330.05260.8781-0.03990.755597.4180.557112.2014
73.1733-0.24261.89119.9113.832.7332-0.00470.01130.0836-0.34710.0701-1.0719-1.79212.2574-0.27040.6103-0.090.01330.89570.06830.773458.825479.2209-6.5364
88.42833.3149-2.66326.3366-5.314.41481.07120.2646-0.0450.93191.75611.4368-0.2243-0.9481-2.04810.73580.18920.02380.8494-0.16291.286788.472579.60468.624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain A and (resid 38 through 103 )
3X-RAY DIFFRACTION3chain A and (resid 104 through 159 )
4X-RAY DIFFRACTION4chain A and (resid 160 through 230 )
5X-RAY DIFFRACTION5chain B and (resid 1 through 111 )
6X-RAY DIFFRACTION6chain B and (resid 112 through 230 )
7X-RAY DIFFRACTION7chain C and (resid 332 through 341 )
8X-RAY DIFFRACTION8chain D and (resid 332 through 341 )

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