[English] 日本語
Yorodumi
- PDB-2wtk: Structure of the heterotrimeric LKB1-STRADalpha-MO25alpha complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wtk
TitleStructure of the heterotrimeric LKB1-STRADalpha-MO25alpha complex
Components
  • CALCIUM-BINDING PROTEIN 39
  • SERINE/THREONINE-PROTEIN KINASE 11Serine/threonine-specific protein kinase
  • 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 / LRR domain binding / negative regulation of potassium ion transmembrane transporter activity / AMPK inhibits chREBP transcriptional activation activity / negative regulation of potassium ion transmembrane transport / dendrite extension / negative regulation of epithelial cell proliferation involved in prostate gland development / serine/threonine protein kinase complex ...positive regulation of vesicle transport along microtubule / intracellular protein-containing complex / Golgi localization / LRR domain binding / negative regulation of potassium ion transmembrane transporter activity / AMPK inhibits chREBP transcriptional activation activity / negative regulation of potassium ion transmembrane transport / dendrite extension / negative regulation of epithelial cell proliferation involved in prostate gland development / serine/threonine protein kinase complex / cellular hypotonic response / tissue homeostasis / 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 / vasculature development / G1 to G0 transition / anoikis / negative regulation of cold-induced thermogenesis / regulation of Wnt signaling pathway / response to glucagon / FOXO-mediated transcription of cell death genes / response to ionizing radiation / 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 / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of autophagy / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein export from nucleus / protein serine/threonine kinase activator activity / axonogenesis / protein dephosphorylation / response to activity / positive regulation of peptidyl-threonine phosphorylation / regulation of signal transduction by p53 class mediator / regulation of cell growth / peptidyl-threonine phosphorylation / negative regulation of canonical Wnt signaling pathway / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / Z disc / autophagy / kinase binding / positive regulation of protein localization to nucleus / p53 binding / glucose homeostasis / T cell receptor signaling pathway / spermatogenesis / peptidyl-serine phosphorylation / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / protein autophosphorylation / regulation of cell cycle / non-specific serine/threonine protein kinase / intracellular signal transduction / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / Neutrophil degranulation / protein-containing complex binding / magnesium ion binding / signal transduction / mitochondrion / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / 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 / Transferase(Phosphotransferase) 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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 / Serine/threonine-specific protein kinase / 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

-
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 / Sulfate


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


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

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more