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- PDB-4fzf: Crystal structure of MST4-MO25 complex with DKI -

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Basic information

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


negative regulation of potassium ion transmembrane transporter activity / microvillus assembly / negative regulation of potassium ion transmembrane transport / FAR/SIN/STRIPAK complex / serine/threonine protein kinase complex / cellular hypotonic response / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / vesicle membrane / Golgi-associated vesicle ...negative regulation of potassium ion transmembrane transporter activity / microvillus assembly / negative regulation of potassium ion transmembrane transport / FAR/SIN/STRIPAK complex / serine/threonine protein kinase complex / cellular hypotonic response / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / vesicle membrane / Golgi-associated vesicle / protein kinase activator activity / Apoptotic cleavage of cellular proteins / cellular response to starvation / protein serine/threonine kinase activator activity / negative regulation of cell migration / positive regulation of peptidyl-threonine phosphorylation / cell periphery / response to activity / positive regulation of protein serine/threonine kinase activity / kinase binding / Z disc / cellular response to oxidative stress / peptidyl-serine phosphorylation / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / apical plasma membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-DKI / Serine/threonine-protein kinase 26 / Calcium-binding protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 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)70,6673
Polymers70,2422
Non-polymers4251
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-9 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.464, 239.464, 239.464
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-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2

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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: 4.07 Å3/Da / Density % sol: 69.8 %
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: Sep 10, 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: 3.64→50 Å / Num. all: 13410 / Num. obs: 13356 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.8 %
Reflection shellResolution: 3.64→3.71 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 651 / % 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: 3.64→38.85 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.831 / SU B: 73.766 / SU ML: 0.499 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.715 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30916 657 4.9 %RANDOM
Rwork0.25214 ---
all0.25515 12760 --
obs0.25515 12643 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.313 Å2
Refinement stepCycle: LAST / Resolution: 3.64→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4859 0 28 0 4887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024979
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9796717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33225.279233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.77315937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2791521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213694
LS refinement shellResolution: 3.644→3.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 45 -
Rwork0.261 811 -
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)
17.65430.80912.64952.21990.23112.9831-0.37550.04191.7843-0.3796-0.03430.6999-0.7163-0.11870.40991.0552-0.1587-0.02710.777-0.34581.392642.2412-73.22970.0213
22.81680.4395-0.82853.33231.22336.51710.2595-0.14620.30610.03640.29810.2663-0.61940.336-0.55760.2504-0.089-0.08830.276-0.11460.390339.2795-103.7564-13.3534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 334
2X-RAY DIFFRACTION2B17 - 297
3X-RAY DIFFRACTION2B301

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