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- PDB-3zhp: Human MST3 (STK24) in complex with MO25beta -

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Basic information

Entry
Database: PDB / ID: 3zhp
TitleHuman MST3 (STK24) in complex with MO25beta
Components
  • CALCIUM-BINDING PROTEIN 39-LIKE
  • SERINE/THREONINE-PROTEIN KINASE 24
KeywordsCELL CYCLE / MO25
Function / homology
Function and homology information


regulation of cell cycle => GO:0051726 / Apoptotic execution phase / regulation of axon regeneration / Energy dependent regulation of mTOR by LKB1-AMPK / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / protein serine/threonine kinase activator activity ...regulation of cell cycle => GO:0051726 / Apoptotic execution phase / regulation of axon regeneration / Energy dependent regulation of mTOR by LKB1-AMPK / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / protein serine/threonine kinase activator activity / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / 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 / Armadillo-type fold ...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
Calcium-binding protein 39-like / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsElkins, J.M. / Szklarz, M. / Krojer, T. / Mehellou, Y. / Alessi, D.R. / Chaikaud, A. / von Delft, F. / Bountra, C. / Edwards, A. / Knapp, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Structural Insights Into the Activation of Mst3 by Mo25.
Authors: Mehellou, Y. / Alessi, D.R. / Macartney, T.J. / Szklarz, M. / Knapp, S. / Elkins, J.M.
History
DepositionDec 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Jul 16, 2014Group: Structure summary
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALCIUM-BINDING PROTEIN 39-LIKE
B: CALCIUM-BINDING PROTEIN 39-LIKE
C: SERINE/THREONINE-PROTEIN KINASE 24
D: SERINE/THREONINE-PROTEIN KINASE 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5498
Polymers145,1654
Non-polymers3844
Water00
1
A: CALCIUM-BINDING PROTEIN 39-LIKE
D: SERINE/THREONINE-PROTEIN KINASE 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7754
Polymers72,5832
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8.1 kcal/mol
Surface area32860 Å2
MethodPISA
2
B: CALCIUM-BINDING PROTEIN 39-LIKE
C: SERINE/THREONINE-PROTEIN KINASE 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7754
Polymers72,5832
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-6.4 kcal/mol
Surface area33800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 120.340, 98.910
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.24846, 0.96801, 0.03509), (0.96864, -0.24827, -0.00978), (-0.00076, 0.03642, -0.99934)51.2346, -49.251, 56.81429
2given(0.27547, 0.95793, 0.08058), (0.9598, -0.27876, 0.0327), (0.05378, 0.06834, -0.99621)34.00862, -64.12675, 54.89547

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Components

#1: Protein CALCIUM-BINDING PROTEIN 39-LIKE / ANTIGEN MLAA-34 / MO25BETA / MO25-LIKE PROTEIN


Mass: 39279.562 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H9S4
#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: 33303.047 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 19-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 2.62 Å3/Da / Density % sol: 53.15 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M NA/KPO4, 10% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorDate: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.9→63.88 Å / Num. obs: 32108 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 69.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.7 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3CKW 3GNI 1UPK 2WTK

3ckw

3gni

1upk

2wtk


Resolution: 2.9→51.88 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.383
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1627 5.07 %RANDOM
Rwork0.2267 ---
obs0.2284 32082 96.54 %-
Displacement parametersBiso mean: 124.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.8757 Å20 Å2-28.3452 Å2
2---15.1949 Å20 Å2
3---16.0706 Å2
Refine analyzeLuzzati coordinate error obs: 0.771 Å
Refinement stepCycle: LAST / Resolution: 2.9→51.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8787 0 20 0 8807
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098971HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9912223HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4087SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes206HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1305HARMONIC5
X-RAY DIFFRACTIONt_it8971HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion2.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1272SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10473SEMIHARMONIC4
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2912 141 4.74 %
Rwork0.2987 2834 -
all0.2984 2975 -
obs--96.54 %
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)
16.17864.41655.83946.67385.03538.06050.0720.25360.03270.01720.10780.1674-0.0484-0.2229-0.17990.4654-0.2459-0.29520.4692-0.35030.3127.3841-66.873141.3905
27.24460.74832.82824.0871.40234.42960.42510.9277-0.9993-0.263-0.1968-0.33990.32230.1532-0.2283-0.05650.065-0.1189-0.335-0.2302-0.047230.5086-56.091862.8369
30.81492.87660.95154.4456-0.402410.8728-0.013-0.32730.1731-0.04740.01320.1622-0.3176-0.2003-0.0002-0.1923-0.0798-0.2342-0.3259-0.16070.267743.1109-36.542782.249
48.0433-1.1741-0.50354.1395-3.42477.86160.0252-0.2226-0.14790.15440.05630.17540.0818-0.2125-0.08150.1441-0.1530.07470.605-0.00010.3079-10.144-26.285412.95
55.8381.93160.54924.8092-0.10782.5343-0.6670.05410.8659-0.61980.08240.717-0.5421-0.50880.5846-0.21320.1323-0.2732-0.2691-0.28580.11066.6812-6.6528-7.8067
67.40573.1039-1.38781.74352.98727.9699-0.01220.19730.0009-0.09490.0076-0.08740.02250.01410.00470.2982-0.1613-0.03270.31890.17070.15729.86180.1212-26.0943
75.37650.36270.71148.03731.90963.01640.0476-0.98690.48080.2657-0.1482-0.4328-0.0042-0.10540.1005-0.30040.039-0.1886-0.0839-0.23180.052626.0002-18.74876.7718
83.76840.1850.69366.8548-0.11216.28590.3419-0.3782-0.77460.0875-0.5045-0.41530.63050.53290.1626-0.35140.048-0.147-0.30790.0710.110424.7638-39.967-1.9363
93.4674-2.51011.15617.9367-4.64975.03290.03950.92990.1952-0.5755-0.44870.0182-0.44410.0490.40910.56210.0263-0.02810.34180.0137-0.379423.6293-33.819348.0678
107.5737-3.84031.94894.1652-0.83835.94620.09640.7438-0.2924-0.4502-0.11681.0274-0.5667-0.79340.0205-0.00970.2546-0.32750.11720.06940.07452.5545-29.214355.4019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|13 - A|79 }
2X-RAY DIFFRACTION2{ A|80 - A|295 }
3X-RAY DIFFRACTION3{ A|296 - A|333 }
4X-RAY DIFFRACTION4{ B|13 - B|79 }
5X-RAY DIFFRACTION5{ B|80 - B|295 }
6X-RAY DIFFRACTION6{ B|296 - B|332 }
7X-RAY DIFFRACTION7{ C|33 - C|113 }
8X-RAY DIFFRACTION8{ C|114 - C|288 }
9X-RAY DIFFRACTION9{ D|33 - D|113 }
10X-RAY DIFFRACTION10{ D|114 - D|289 }

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