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- PDB-4nzw: Crystal Structure of STK25-MO25 Complex -

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Basic information

Entry
Database: PDB / ID: 4nzw
TitleCrystal Structure of STK25-MO25 Complex
Components
  • Calcium-binding protein 39
  • Serine/threonine-protein kinase 25
KeywordsTRANSFERASE ACTIVATOR/TRANSFERASE / scafolding protein / Ser/Thr protein kinase / TRANSFERASE ACTIVATOR-TRANSFERASE complex
Function / homology
Function and homology information


intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / negative regulation of potassium ion transmembrane transport / response to thyroid hormone / Golgi reassembly / FAR/SIN/STRIPAK complex / positive regulation of stress-activated MAPK cascade / cellular hypotonic response / establishment of Golgi localization / Energy dependent regulation of mTOR by LKB1-AMPK ...intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / negative regulation of potassium ion transmembrane transport / response to thyroid hormone / Golgi reassembly / FAR/SIN/STRIPAK complex / positive regulation of stress-activated MAPK cascade / cellular hypotonic response / establishment of Golgi localization / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / positive regulation of axonogenesis / establishment or maintenance of cell polarity / positive regulation of protein serine/threonine kinase activity / protein kinase activator activity / axonogenesis / protein serine/threonine kinase binding / protein serine/threonine kinase activator activity / response to activity / kinase binding / Z disc / protein autophosphorylation / response to oxidative stress / cellular response to oxidative stress / secretory granule lumen / ficolin-1-rich granule lumen / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine kinase 25, catalytic domain / Mo25-like / Mo25-like / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Serine/threonine kinase 25, catalytic domain / Mo25-like / Mo25-like / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / 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 / 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
Chem-J60 / Serine/threonine-protein kinase 25 / Calcium-binding protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.583 Å
AuthorsFeng, M. / Hao, Q. / Zhou, Z.C.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Structural insights into regulatory mechanisms of MO25-mediated kinase activation.
Authors: Hao, Q. / Feng, M. / Shi, Z. / Li, C. / Chen, M. / Wang, W. / Zhang, M. / Jiao, S. / Zhou, Z.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Calcium-binding protein 39
B: Serine/threonine-protein kinase 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7853
Polymers72,3702
Non-polymers4151
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-22 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.718, 116.718, 126.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Calcium-binding protein 39 / MO25alpha / Protein Mo25


Mass: 38665.496 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 8-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAB39, CGI-66, MO25 / Plasmid: pET28a-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y376
#2: Protein Serine/threonine-protein kinase 25 / Ste20-like kinase / Sterile 20/oxidant stress-response kinase 1 / SOK-1 / Ste20/oxidant stress ...Ste20-like kinase / Sterile 20/oxidant stress-response kinase 1 / SOK-1 / Ste20/oxidant stress response kinase 1


Mass: 33704.703 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP RESIDUES 1-293 / Mutation: D158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOK1, STK25, YSK1 / Plasmid: pET28a-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O00506, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-J60 / 5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE


Mass: 414.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27ClN4O2

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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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES PH 7.0, 1M SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2012
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: 3.583→50 Å / Num. all: 10784 / Num. obs: 10753 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 15.9
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 5.25 / % possible all: 98.45

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XIK, 1UPL

2xik

1upl


Resolution: 3.583→40.299 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 1065 9.9 %RANDOM
Rwork0.2074 ---
all0.2141 ---
obs0.2141 10753 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.583→40.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 29 0 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024811
X-RAY DIFFRACTIONf_angle_d0.8086484
X-RAY DIFFRACTIONf_dihedral_angle_d13.3541831
X-RAY DIFFRACTIONf_chiral_restr0.044723
X-RAY DIFFRACTIONf_plane_restr0.002816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5826-3.74560.31041300.2502115999
3.7456-3.94290.29451350.221173100
3.9429-4.18970.30411270.21461196100
4.1897-4.51280.27331360.1891194100
4.5128-4.96620.26041310.17891196100
4.9662-5.68310.25841290.19881224100
5.6831-7.15350.32121360.23871226100
7.1535-40.30130.25091410.20211320100

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