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- PDB-4fza: Crystal structure of MST4-MO25 complex -

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Basic information

Entry
Database: PDB / ID: 4fza
TitleCrystal structure of MST4-MO25 complex
Components
  • Calcium-binding protein 39
  • Serine/threonine-protein kinase MST4
KeywordsSIGNALING PROTEIN/TRANSFERASE / Scaffold protein / Protein Ser/Thr kinase / ATP binding / SIGNALING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


microvillus assembly / negative regulation of potassium ion transmembrane transport / response to thyroid hormone / FAR/SIN/STRIPAK complex / cellular hypotonic response / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / vesicle membrane / Golgi-associated vesicle / Apoptotic cleavage of cellular proteins ...microvillus assembly / negative regulation of potassium ion transmembrane transport / response to thyroid hormone / FAR/SIN/STRIPAK complex / cellular hypotonic response / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / vesicle membrane / Golgi-associated vesicle / Apoptotic cleavage of cellular proteins / positive regulation of protein serine/threonine kinase activity / protein kinase activator activity / protein serine/threonine kinase binding / negative regulation of cell migration / cellular response to starvation / protein serine/threonine kinase activator activity / response to activity / cell periphery / kinase binding / Z disc / protein autophosphorylation / cellular response to oxidative stress / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / apical plasma membrane / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / magnesium ion binding / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
MST4, kinase 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 ...MST4, kinase 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
Serine/threonine-protein kinase 26 / Calcium-binding protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsShi, Z.B. / Zhou, Z.C.
CitationJournal: Structure / Year: 2013
Title: Structure of the MST4 in Complex with MO25 Provides Insights into Its Activation Mechanism
Authors: Shi, Z. / Jiao, S. / Zhang, Z. / Ma, M. / Zhang, Z. / Chen, C. / Wang, K. / Wang, H. / Wang, W. / Zhang, L. / Zhao, Y. / Zhou, Z.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Nov 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 MST4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5185
Polymers70,2422
Non-polymers2763
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-5 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)237.583, 237.583, 237.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

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


Mass: 38311.098 Da / Num. of mol.: 1 / Fragment: Mo25-like, UNP residues 11-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAB39, MO25, CGI-66 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y376
#2: Protein Serine/threonine-protein kinase MST4 / Mammalian STE20-like protein kinase 4 / MST-4 / Mst3 and SOK1-related kinase / STE20-like kinase ...Mammalian STE20-like protein kinase 4 / MST-4 / Mst3 and SOK1-related kinase / STE20-like kinase MST4 / Serine/threonine-protein kinase MASK


Mass: 31930.670 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP residues 18-297 / Mutation: D162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST4, MASK / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9P289, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8.0, 20% PEG 350 mme, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Jul 11, 2011
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: 3.15→50 Å / Num. all: 20053 / Num. obs: 20033 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 19.9 % / Mean I/σ(I) obs: 4 / Num. unique all: 980 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1UPL and 3GGF

1upl

3ggf


Resolution: 3.15→40.75 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 38.699 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25162 1019 5.1 %RANDOM
Rwork0.20601 ---
all0.20835 19018 --
obs0.20835 18854 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.584 Å2
Refinement stepCycle: LAST / Resolution: 3.15→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 18 12 4900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024976
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9746707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.51525.127236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.06115931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7331523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213686
LS refinement shellResolution: 3.153→3.235 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 70 -
Rwork0.276 1227 -
obs--99.62 %
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)
15.3158-2.150.7672.1253-0.4442.2763-0.4178-1.183-0.11760.44110.37380.301-0.36-0.45650.04390.4540.11550.08240.61960.1890.403141.82550.134-72.2792
21.39160.47280.12372.8214-0.41171.71510.0496-0.1114-0.2150.413-0.23550.0650.1109-0.02280.18580.13160.02780.04070.16590.0870.189439.20413.2165-102.8459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 334
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION2B17 - 297
4X-RAY DIFFRACTION2B301 - 303
5X-RAY DIFFRACTION2B1001 - 1011

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