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- PDB-4lg4: Structural Basis for Autoactivation of Human Mst2 Kinase and Its ... -

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Entry
Database: PDB / ID: 4lg4
TitleStructural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5
ComponentsSerine/threonine-protein kinase 3Serine/threonine-specific protein kinase
KeywordsSIGNALING PROTEIN / Hippo / Mst autoactivation / dimerization
Function / homology
Function and homology information


cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome ...cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome / organ growth / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / canonical Wnt signaling pathway / positive regulation of fat cell differentiation / JNK cascade / protein serine/threonine kinase activator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epithelial cell proliferation / central nervous system development / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / protein import into nucleus / positive regulation of DNA-binding transcription factor activity / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53-like tetramerisation domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53-like tetramerisation domain superfamily / 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
Serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsLuo, X. / Ni, L. / Tomchick, D.R.
CitationJournal: Structure / Year: 2013
Title: Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5.
Authors: Ni, L. / Li, S. / Yu, J. / Min, J. / Brautigam, C.A. / Tomchick, D.R. / Pan, D. / Luo, X.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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: Serine/threonine-protein kinase 3
B: Serine/threonine-protein kinase 3
C: Serine/threonine-protein kinase 3
D: Serine/threonine-protein kinase 3
E: Serine/threonine-protein kinase 3
F: Serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,20010
Polymers203,8326
Non-polymers3684
Water2,162120
1
A: Serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3405
Polymers33,9721
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)33,9721
Polymers33,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)33,9721
Polymers33,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)33,9721
Polymers33,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)33,9721
Polymers33,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)33,9721
Polymers33,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)227.179, 69.771, 148.082
Angle α, β, γ (deg.)90.000, 108.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Serine/threonine-protein kinase 3 / Serine/threonine-specific protein kinase / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1 / Serine/threonine-protein kinase 3 36kDa subunit / MST2/N / Serine/threonine-protein kinase 3 20kDa subunit / MST2/C


Mass: 33972.012 Da / Num. of mol.: 6 / Fragment: kinase domain, UNP residues 16-313 / Mutation: D146N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13188, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / pH: 7.7
Details: 0.2 M sodium citrate, 15% (w/v) PEG 3350, 0.1 M HEPES, pH 7.7, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009 / Details: MONOCHROMATOR
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.415→140.342 Å / Num. obs: 83850 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.4
Reflection scaleGroup code: 1
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.7 / % possible all: 91.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3COM

3com


Resolution: 2.42→29.83 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1997 2.38 %
Rwork0.193 --
obs0.194 83826 99.49 %
all-83949 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.4 Å2
Refinement stepCycle: LAST / Resolution: 2.42→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13295 0 24 120 13439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213457
X-RAY DIFFRACTIONf_angle_d0.64518184
X-RAY DIFFRACTIONf_dihedral_angle_d12.4475103
X-RAY DIFFRACTIONf_chiral_restr0.0392044
X-RAY DIFFRACTIONf_plane_restr0.0032303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.48050.32421340.26395491X-RAY DIFFRACTION94
2.4805-2.54750.33151400.23955751X-RAY DIFFRACTION100
2.5475-2.62240.27931420.22555844X-RAY DIFFRACTION100
2.6224-2.7070.29181440.22055871X-RAY DIFFRACTION100
2.707-2.80370.24441430.21935840X-RAY DIFFRACTION100
2.8037-2.91590.28391420.21885854X-RAY DIFFRACTION100
2.9159-3.04850.27941440.21765854X-RAY DIFFRACTION100
3.0485-3.2090.25711420.21785844X-RAY DIFFRACTION100
3.209-3.40980.24761420.20945849X-RAY DIFFRACTION100
3.4098-3.67260.23531450.19175893X-RAY DIFFRACTION100
3.6726-4.04140.1941420.17835836X-RAY DIFFRACTION100
4.0414-4.62440.20391450.15595929X-RAY DIFFRACTION100
4.6244-5.81910.2171450.1815947X-RAY DIFFRACTION100
5.8191-29.8320.20081470.18746026X-RAY DIFFRACTION99
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)
10.8081-0.43660.21230.1976-0.03850.0837-0.1725-0.04581.2144-0.04790.0914-0.6363-0.4514-0.06270.00310.44810.05940.04330.3540.01650.631342.059353.253857.8047
20.1005-0.12720.13880.1314-0.07010.0122-0.00560.1216-0.0139-0.0403-0.23570.0314-0.0051-0.5563-0.00530.38380.12540.00850.3422-0.01510.335533.509742.462453.4968
30.63740.16740.38080.13530.30630.8594-0.05310.01430.12650.01440.1213-0.0506-0.0467-0.0711-00.35130.03250.06640.2640.01540.372547.734634.472853.3006
40.65910.252-0.13070.30720.24021.156-0.02840.16940.2608-0.11480.04950.0219-0.0003-0.2286-00.3350.00710.02340.27730.04360.264542.336330.163140.0802
50.1884-0.15520.23120.1780.06890.39770.15220.1763-0.34720.18970.0089-0.15470.62210.05540.00480.5271-0.00350.01540.2329-0.02040.365447.792315.647646.5878
60.08460.12010.05930.15120.18690.27210.0357-0.37270.49270.20740-0.4529-0.05230.19290.01010.372-0.01850.05010.2067-0.06020.565360.500442.011656.7315
70.16130.17680.09661.1456-0.02850.2360.1847-0.715-0.3091-0.1157-0.209-0.0646-0.2093-0.59510.01280.495-0.0694-0.11071.03770.06160.400263.814150.60816.9807
81.5150.6259-0.33451.537-0.22081.26980.00010.07670.0918-0.0087-0.06150.04320.0284-0.040400.40810.0178-0.02030.48520.06480.251546.26640.19279.1969
90.26690.1320.04460.13150.11760.08350.09411.1083-0.5586-0.05370.0051-0.3328-0.11010.21610.020.70250.02040.03011.23240.14370.588183.485845.297515.3246
100.3830.02210.19810.01670.07070.16180.02690.48140.41530.14650.3385-0.02960.139-0.29080.01820.4442-0.0944-0.07490.74130.24950.582777.863645.459829.645
110.45460.26710.12750.3696-0.47280.4442-0.12110.46430.46170.0050.13740.012-0.05270.16230.00190.30380.0186-0.04380.59120.10130.509189.372747.520834.0918
120.0926-0.13230.05990.3321-0.32540.3612-0.08040.17540.3792-0.03950.1680.31290.14190.013600.30240.02540.00070.3356-0.01410.451382.748139.405946.7156
130.1469-0.15570.0170.0153-0.04010.1056-0.1318-0.0673-0.5908-0.1540.0622-0.4462-0.10130.0197-00.35410.0813-0.00440.3846-0.02390.515394.998534.123953.2908
140.1594-0.03850.20310.16640.13410.2976-0.1785-0.31970.88910.32050.1295-0.1024-0.20620.1363-0.00010.49170.0517-0.07710.4613-0.12580.746394.877452.449153.383
15-0.011-0.05160.0590.0443-0.07930.25460.40740.61460.3704-0.3825-0.1043-0.4916-0.65260.1817-0.00480.39020.18960.05930.95750.01820.5341102.839342.48725.0079
161.1140.20270.1655-0.03940.20620.30981.0894-0.0262-1.91260.3926-0.57710.26260.4633-0.61910.14550.21750.51070.15670.4669-0.70620.836289.43046.228132.1345
172.65410.4282-0.51370.96110.26460.81440.0868-0.1119-0.96960.236-0.0295-0.40250.1890.09960.02990.4270.1072-0.13350.25540.00910.767175.3888.686750.7249
180.00640.0265-0.03540.08980.01520.0073-0.1504-0.609-0.75820.17190.31-0.05760.5533-0.0161-01.01160.03240.04480.85630.00371.5645-3.244939.719529.4073
190.91950.0222-0.69950.9181-0.47471.769-0.21581.0256-0.4893-0.48060.1495-0.1860.12910.403-1.25820.59810.10590.02691.2159-0.47550.578310.541357.421518.7399
200.51-0.5282-0.4650.02750.12170.8230.27380.3598-0.3795-0.0551-0.24790.25650.21360.19120.01320.35680.1958-0.07250.3676-0.07860.501919.67658.999158.0898
211.20250.61320.8540.90970.04971.9014-0.1010.2460.0745-0.02240.0270.1333-0.11990.4233-0.00330.26090.00790.03020.28990.0630.237512.663180.121152.393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 235 )
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 283 )
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 308 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 305 )
9X-RAY DIFFRACTION9chain 'C' and (resid 18 through 51 )
10X-RAY DIFFRACTION10chain 'C' and (resid 52 through 84 )
11X-RAY DIFFRACTION11chain 'C' and (resid 85 through 162 )
12X-RAY DIFFRACTION12chain 'C' and (resid 163 through 216 )
13X-RAY DIFFRACTION13chain 'C' and (resid 217 through 248 )
14X-RAY DIFFRACTION14chain 'C' and (resid 249 through 283 )
15X-RAY DIFFRACTION15chain 'C' and (resid 284 through 307 )
16X-RAY DIFFRACTION16chain 'D' and (resid 26 through 106 )
17X-RAY DIFFRACTION17chain 'D' and (resid 107 through 308 )
18X-RAY DIFFRACTION18chain 'E' and (resid 18 through 74 )
19X-RAY DIFFRACTION19chain 'E' and (resid 75 through 302 )
20X-RAY DIFFRACTION20chain 'F' and (resid 18 through 119 )
21X-RAY DIFFRACTION21chain 'F' and (resid 120 through 308 )

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