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- PDB-4o27: Crystal structure of MST3-MO25 complex with WIF motif -

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Basic information

Entry
Database: PDB / ID: 4o27
TitleCrystal structure of MST3-MO25 complex with WIF motif
Components
  • 5-mer peptide from serine/threonine-protein kinase 24
  • Calcium-binding protein 39
  • Serine/threonine-protein kinase 24
KeywordsTRANSFERASE ACTIVATOR/TRANSFERASE / Scaffold protein / Protein Ser/Thr kinase / TRANSFERASE ACTIVATOR-TRANSFERASE complex / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of potassium ion transmembrane transport / Apoptotic execution phase / response to thyroid hormone / FAR/SIN/STRIPAK complex / cellular hypotonic response / regulation of axon regeneration / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis ...negative regulation of potassium ion transmembrane transport / Apoptotic execution phase / response to thyroid hormone / FAR/SIN/STRIPAK complex / cellular hypotonic response / regulation of axon regeneration / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / 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 / kinase binding / Z disc / protein autophosphorylation / 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 / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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
ADENOSINE-5'-DIPHOSPHATE / : / Calcium-binding protein 39 / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.185 Å
AuthorsHao, Q. / Feng, M. / 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 16, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Calcium-binding protein 39
B: Serine/threonine-protein kinase 24
C: 5-mer peptide from serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2105
Polymers70,7283
Non-polymers4822
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.111, 119.111, 149.258
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: 38053.785 Da / Num. of mol.: 1 / Fragment: Mo25-like, UNP residues 11-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAB39, CGI-66, MO25 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y376
#2: Protein Serine/threonine-protein kinase 24 / Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3 / Serine/threonine-protein kinase 24 36 kDa subunit / Mammalian STE20-like protein kinase 3 N-terminal / MST3/N / Serine/threonine-protein kinase 24 12 kDa subunit / Mammalian STE20-like protein kinase 3 C-terminal / MST3/C


Mass: 31965.729 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP residues 30-309 / Mutation: T190E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST3, STK24, STK3 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase
#3: Protein/peptide 5-mer peptide from serine/threonine-protein kinase 24


Mass: 708.758 Da / Num. of mol.: 1 / Fragment: WIF motif, UNP residues 336-340 / Mutation: T340E / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

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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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 2.0M Ammonium sulfate, VAPOR DIFFUSION, SITTING 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: Apr 15, 2012
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: 3.185→50 Å / Num. all: 18586 / Num. obs: 18586 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 4.84 / % possible all: 100

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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: 3A7J, 1UPL

3a7j

1upl


Resolution: 3.185→46.55 Å / SU ML: 0.44 / σ(F): 1.35 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 1853 10 %RANDOM
Rwork0.1965 ---
all0.203 18579 --
obs0.203 18533 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.9 Å2
Refinement stepCycle: LAST / Resolution: 3.185→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4813 0 28 0 4841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014966
X-RAY DIFFRACTIONf_angle_d1.2756728
X-RAY DIFFRACTIONf_dihedral_angle_d16.9731840
X-RAY DIFFRACTIONf_chiral_restr0.048766
X-RAY DIFFRACTIONf_plane_restr0.006857
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.185-3.27110.3921350.2957121597
3.2711-3.36730.33061390.26261255100
3.3673-3.4760.30431410.241266100
3.476-3.60020.36461410.23131263100
3.6002-3.74430.27421410.23031276100
3.7443-3.91460.24211390.19851254100
3.9146-4.12090.30351410.19441272100
4.1209-4.37890.22931420.17921276100
4.3789-4.71670.25441410.17061276100
4.7167-5.19080.23271450.17961298100
5.1908-5.94060.28961450.21761302100
5.9406-7.47950.2681470.21311324100
7.4795-46.55490.21611560.1659140399

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