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- PDB-6ao5: Crystal structure of human MST2 in complex with SAV1 SARAH domain -

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Basic information

Entry
Database: PDB / ID: 6ao5
TitleCrystal structure of human MST2 in complex with SAV1 SARAH domain
Components
  • Protein salvador homolog 1
  • Serine/threonine-protein kinase 3
KeywordsSIGNALING PROTEIN / Hippo / mst autoactivation / dimerization
Function / homology
Function and homology information


keratinocyte apoptotic process / regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / intestinal epithelial cell differentiation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of stem cell population maintenance / positive regulation of keratinocyte apoptotic process / positive regulation of hippo signaling ...keratinocyte apoptotic process / regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / intestinal epithelial cell differentiation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of stem cell population maintenance / positive regulation of keratinocyte apoptotic process / positive regulation of hippo signaling / endocardium development / negative regulation of cardiac muscle cell proliferation / negative regulation of organ growth / lung epithelial cell differentiation / hippo signaling / transcription regulator activator activity / Signaling by Hippo / protein localization to centrosome / cardiac muscle cell proliferation / organ growth / ventricular septum morphogenesis / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / hair follicle development / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / keratinocyte differentiation / JNK cascade / protein serine/threonine kinase activator activity / central nervous system development / epithelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / protein import into nucleus / negative regulation of epithelial cell proliferation / molecular adaptor activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Scaffold protein salvador / : / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / : / p53-like tetramerisation domain superfamily ...Scaffold protein salvador / : / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / : / p53-like tetramerisation domain superfamily / WW domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Few Secondary Structures / Irregular / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase 3 / Protein salvador homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å
AuthorsTomchick, D.R. / Luo, X. / Ni, L.
Citation
Journal: Elife / Year: 2017
Title: SAV1 promotes Hippo kinase activation through antagonizing the PP2A phosphatase STRIPAK.
Authors: Bae, S.J. / Ni, L. / Osinski, A. / Tomchick, D.R. / Brautigam, C.A. / Luo, X.
#1: Journal: 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
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 3
B: Protein salvador homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5354
Polymers53,0052
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mutagenesis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-42 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.678, 223.678, 79.645
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Serine/threonine-protein kinase 3 / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1


Mass: 41733.961 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 16-313, 428-491) / Mutation: D146N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Plasmid: PET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13188, non-specific serine/threonine protein kinase
#2: Protein Protein salvador homolog 1 / 45 kDa WW domain protein / hWW45


Mass: 11270.966 Da / Num. of mol.: 1 / Fragment: SARAH domain (UNP residues 291-383)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAV1, WW45 / Plasmid: PET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H4B6
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.62 Å3/Da / Density % sol: 65.99 % / Mosaicity: 0.579 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M NaCl, 0.1 M Hepes, 0.19 mM CYMAL-7, 1 mM TCEP, 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 15976 / % possible obs: 99.9 % / Redundancy: 19 % / Biso Wilson estimate: 48.45 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.029 / Rrim(I) all: 0.128 / Χ2: 1.085 / Net I/σ(I): 7 / Num. measured all: 303392
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3121.7157630.8410.4831.7880.85898.5
3-3.0613.91.587950.8360.4221.6380.85799.7
3.06-3.11161.6687840.8890.4211.7220.863100
3.11-3.18181.2478010.9290.31.2830.887100
3.18-3.2519.41.0417920.9520.2411.0680.883100
3.25-3.32200.8058000.9740.1840.8260.897100
3.32-3.4120.50.687860.9730.1530.6980.907100
3.41-3.520.30.5397980.9810.1220.5530.951100
3.5-3.620.40.4017940.990.090.4110.955100
3.6-3.7220.40.2987910.9930.0680.3061.047100
3.72-3.8520.40.2438030.9960.0550.251100
3.85-420.30.1898000.9970.0430.1941.067100
4-4.1920.20.1488070.9980.0340.1521.117100
4.19-4.4120.30.1297950.9980.030.1331.291100
4.41-4.6820.10.1098030.9970.0250.1121.329100
4.68-5.0420.10.1047960.9970.0240.1071.394100
5.04-5.55200.1138020.9970.0260.1161.416100
5.55-6.3519.60.0968130.9940.0230.0991.391100
6.35-819.20.0658140.9990.0150.0671.216100
8-5018.40.0518390.9990.0120.0531.13599.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LGD

4lgd


Resolution: 2.955→42.271 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 650 4.92 %random
Rwork0.2346 12549 --
obs0.2357 13199 82.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.97 Å2 / Biso mean: 60.0404 Å2 / Biso min: 15.87 Å2
Refinement stepCycle: final / Resolution: 2.955→42.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 45 0 3385
Biso mean--40.75 --
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093449
X-RAY DIFFRACTIONf_angle_d0.64655
X-RAY DIFFRACTIONf_chiral_restr0.04509
X-RAY DIFFRACTIONf_plane_restr0.004586
X-RAY DIFFRACTIONf_dihedral_angle_d14.5262101
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9547-3.18270.276520.31841027107934
3.1827-3.50290.3461140.28542335244977
3.5029-4.00940.24991590.245130353194100
4.0094-5.05010.25221610.210330513212100
5.0501-42.27550.23091640.216431013265100
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)
15.5589-1.90110.54585.7248-1.50392.909-0.5487-0.9572-0.44980.65090.0023-0.18340.2358-0.04630.4440.68780.23330.1160.5879-0.18280.852945.276487.559817.5114
21.0834-0.0375-0.37170.66550.21551.0266-0.06920.1282-0.2918-0.04520.0978-0.10920.23620.1396-0.02130.2660.08190.10010.1639-0.33420.185940.638100.823913.8865
33.406-0.2983-0.78320.82250.42741.72760.16250.22770.75950.1350.0595-0.0818-0.3810.1998-0.20240.33130.0480.06290.2489-0.02210.30542.4784111.267612.4692
43.08931.4864-0.02242.0634-0.36430.8074-0.06910.22940.16730.01350.04910.61780.3856-0.2974-0.07620.2835-0.25190.16030.4005-0.05520.332276.892386.590534.2521
51.250.29652.05460.64840.1943.5228-0.05990.2789-0.1323-0.70920.1175-0.18560.91170.9522-0.06040.72880.1026-0.05020.410.01390.319374.621466.38242.833
63.482.25780.09933.72170.31872.4503-0.0901-0.1255-0.3093-0.0644-0.05630.17790.48690.05320.19220.3008-0.04770.09970.3648-0.00120.125780.640181.582237.6746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 84 )A28 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 216 )A85 - 216
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 307 )A217 - 307
4X-RAY DIFFRACTION4chain 'A' and (resid 308 through 488 )A308 - 488
5X-RAY DIFFRACTION5chain 'B' and (resid 291 through 313 )B291 - 313
6X-RAY DIFFRACTION6chain 'B' and (resid 314 through 376 )B314 - 376

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