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- PDB-2wtk: Structure of the heterotrimeric LKB1-STRADalpha-MO25alpha complex -

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Basic information

Entry
Database: PDB / ID: 2wtk
TitleStructure of the heterotrimeric LKB1-STRADalpha-MO25alpha complex
Components
  • CALCIUM-BINDING PROTEIN 39
  • SERINE/THREONINE-PROTEIN KINASE 11
  • STE20-RELATED KINASE ADAPTER PROTEIN ALPHA
KeywordsTRANSFERASE/METAL-BINDING PROTEIN / TRANSFERASE-METAL-BINDING PROTEIN COMPLEX / TRANSFERASE METAL-BINDING PROTEIN COMPLEX / KINASE / NUCLEUS / SERINE/THREONINE-PROTEIN KINASE / PSEUDOKINASE / PHOSPHOPROTEIN / SIGNAL TRANSDUCTION / TRANSFERASE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


positive regulation of vesicle transport along microtubule / intracellular protein-containing complex / Golgi localization / AMPK inhibits chREBP transcriptional activation activity / negative regulation of potassium ion transmembrane transport / dendrite extension / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to thyroid hormone / negative regulation of epithelial cell proliferation involved in prostate gland development / activation of protein kinase activity ...positive regulation of vesicle transport along microtubule / intracellular protein-containing complex / Golgi localization / AMPK inhibits chREBP transcriptional activation activity / negative regulation of potassium ion transmembrane transport / dendrite extension / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to thyroid hormone / negative regulation of epithelial cell proliferation involved in prostate gland development / activation of protein kinase activity / cellular hypotonic response / tissue homeostasis / epithelial cell proliferation involved in prostate gland development / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / positive thymic T cell selection / vasculature development / positive regulation of axonogenesis / regulation of Wnt signaling pathway / anoikis / G1 to G0 transition / negative regulation of cold-induced thermogenesis / cellular response to UV-B / regulation of dendrite morphogenesis / LRR domain binding / response to ionizing radiation / positive regulation of transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of cell death genes / establishment of cell polarity / intrinsic apoptotic signaling pathway by p53 class mediator / peptidyl-threonine phosphorylation / positive regulation of protein serine/threonine kinase activity / protein kinase activator activity / protein localization to nucleus / protein dephosphorylation / negative regulation of TORC1 signaling / positive regulation of autophagy / axonogenesis / protein serine/threonine kinase binding / protein export from nucleus / regulation of signal transduction by p53 class mediator / protein serine/threonine kinase activator activity / response to activity / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / autophagy / positive regulation of protein localization to nucleus / kinase binding / Z disc / p53 binding / glucose homeostasis / T cell receptor signaling pathway / protein autophosphorylation / secretory granule lumen / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / protein phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / intracellular signal transduction / cilium / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / Neutrophil degranulation / centrosome / magnesium ion binding / signal transduction / mitochondrion / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Serine/Threonine kinase LKB1, catalytic domain / : / Mo25-like / Mo25-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Phosphorylase Kinase; domain 1 ...Serine/Threonine kinase LKB1, catalytic domain / : / Mo25-like / Mo25-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase STK11 / STE20-related kinase adapter protein alpha / Calcium-binding protein 39
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZeqiraj, E. / van Aalten, D.M.F.
CitationJournal: Science / Year: 2009
Title: Structure of the Lkb1-Strad-Mo25 Complex Reveals an Allosteric Mechanism of Kinase Activation.
Authors: Zeqiraj, E. / Filippi, B.M. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionSep 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 2, 2011Group: Database references / Refinement description
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALCIUM-BINDING PROTEIN 39
B: STE20-RELATED KINASE ADAPTER PROTEIN ALPHA
C: SERINE/THREONINE-PROTEIN KINASE 11
D: CALCIUM-BINDING PROTEIN 39
E: STE20-RELATED KINASE ADAPTER PROTEIN ALPHA
F: SERINE/THREONINE-PROTEIN KINASE 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,06311
Polymers231,9426
Non-polymers2,1215
Water1,838102
1
D: CALCIUM-BINDING PROTEIN 39
E: STE20-RELATED KINASE ADAPTER PROTEIN ALPHA
F: SERINE/THREONINE-PROTEIN KINASE 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0806
Polymers115,9713
Non-polymers1,1083
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-40.33 kcal/mol
Surface area40440 Å2
MethodPISA
2
A: CALCIUM-BINDING PROTEIN 39
B: STE20-RELATED KINASE ADAPTER PROTEIN ALPHA
C: SERINE/THREONINE-PROTEIN KINASE 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9845
Polymers115,9713
Non-polymers1,0122
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-33.12 kcal/mol
Surface area41080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.360, 118.360, 390.012
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein CALCIUM-BINDING PROTEIN 39 / MO25ALPHA / PROTEIN MO25


Mass: 39922.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MULTIBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9Y376
#2: Protein STE20-RELATED KINASE ADAPTER PROTEIN ALPHA / STRADALPHA / STRAD ALPHA / STE20-RELATED ADAPTER PROTEIN / SEROLOGICALLY DEFINED BREAST CANCER ...STRADALPHA / STRAD ALPHA / STE20-RELATED ADAPTER PROTEIN / SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-96


Mass: 41748.383 Da / Num. of mol.: 2 / Fragment: PSEUDOKINASE DOMAIN, RESIDUES 59-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MULTIBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q7RTN6
#3: Protein SERINE/THREONINE-PROTEIN KINASE 11 / LKB1 / SERINE/THREONINE-PROTEIN KINASE LKB1 / RENAL CARCINOMA ANTIGEN NY-REN-19


Mass: 34299.797 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 43-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MULTIBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q15831, non-specific serine/threonine protein kinase

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Non-polymers , 3 types, 107 molecules

#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN C, ASP 194 TO ALA ENGINEERED RESIDUE IN CHAIN F, ASP 194 TO ALA

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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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 8.5 / Details: PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 91884 / % possible obs: 99.2 % / Observed criterion σ(I): 2.4 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GNI

3gni


Resolution: 2.65→19.9 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.894 / SU B: 22.414 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 919 1 %RANDOM
Rwork0.24 ---
obs0.24 90835 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å21.29 Å20 Å2
2--2.59 Å20 Å2
3----3.88 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14627 0 121 102 14850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02215060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.98120340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79851788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75524.178687
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.313152724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1391583
X-RAY DIFFRACTIONr_chiral_restr0.0970.22258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111141
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0261.59052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88214631
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.22736008
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0314.55709
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 64 -
Rwork0.304 6540 -
obs--100 %
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)
11.56330.2029-0.50130.5926-0.78946.3089-0.3930.1042-0.2653-0.33650.0006-0.06110.8377-0.16140.39240.4756-0.15450.24750.1079-0.05230.3357-37.590241.807350.0949
210.1531-5.67441.84869.7173-1.97095.1979-0.31190.2660.07840.1448-0.2845-1.13140.47420.24990.59630.9328-0.16310.40990.1321-0.07750.3954-36.324713.096241.5122
31.16550.9161-0.45512.7597-0.23911.17920.00230.0755-0.09030.0865-0.09590.20310.5567-0.12940.09371.1427-0.38870.43930.1752-0.17720.3444-54.107513.330451.9737
40.5080.7454-1.43645.8230.19145.8113-0.26880.37680.1033-0.95960.16960.76740.9605-1.10410.09920.8837-0.5370.1050.8923-0.19580.5752-68.896140.858732.9706
54.071-0.3389-1.29233.9865-0.20532.801-0.53120.32890.11790.03990.34210.13790.3513-0.66190.1890.1309-0.144-0.03560.43080.02720.2447-64.900857.341849.3133
62.3869-0.3384-2.39661.0096-0.50517.9060.2056-0.3436-0.1276-0.2308-0.08330.064-0.46180.9177-0.12240.1588-0.05010.03860.231-0.02650.163-34.0601-31.817817.9668
76.02863.03360.866611.9309-1.19584.8137-0.1204-0.0080.0387-0.2266-0.2571-1.0331-0.52640.49770.37740.7495-0.04360.20260.2311-0.01860.2084-36.3948-3.003625.8417
81.2917-0.1432-0.04562.3703-0.68983.33280.07610.00030.279-0.2170.06060.3676-0.9139-0.4687-0.13670.61440.14230.11380.09170.0310.1963-49.735-4.120112.6435
94.01420.3322-1.16323.3194-1.56134.7682-0.32370.5882-0.14760.21320.65910.60420.0559-1.7469-0.33540.0938-0.14810.00030.98110.22510.2345-63.7277-36.582422.5263
105.6952-0.3977-1.19033.08750.5639.3846-0.59791.204-1.4346-0.46680.35460.37362.7543-1.70760.24321.06-0.84160.04210.9598-0.25950.8309-58.5054-54.729913.717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 336
2X-RAY DIFFRACTION2B61 - 103
3X-RAY DIFFRACTION3B104 - 431
4X-RAY DIFFRACTION4C47 - 132
5X-RAY DIFFRACTION5C133 - 342
6X-RAY DIFFRACTION6D10 - 336
7X-RAY DIFFRACTION7E60 - 90
8X-RAY DIFFRACTION8E91 - 431
9X-RAY DIFFRACTION9F45 - 204
10X-RAY DIFFRACTION10F205 - 324

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