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- PDB-4oh9: Crystal Structure of the human MST2 SARAH homodimer -

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Basic information

Entry
Database: PDB / ID: 4oh9
TitleCrystal Structure of the human MST2 SARAH homodimer
ComponentsSerine/threonine-protein kinase 3
KeywordsTRANSFERASE / SARAH domain / coiled-coil / homodierizarion / heterodimerization
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 / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / 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 / positive regulation of DNA-binding transcription factor activity / protein import into nucleus / 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 / protein-containing complex / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / 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 / Few Secondary Structures / Irregular ...: / 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 / Few Secondary Structures / Irregular / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsHwang, E. / Cheong, H.-K. / Ul Mushtaq, A. / Kim, H.-Y. / Yeo, K.J. / Kim, E. / Lee, W.C. / Hwang, K.Y. / Cheong, C. / Jeon, Y.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis of the heterodimerization of the MST and RASSF SARAH domains in the Hippo signalling pathway.
Authors: Hwang, E. / Cheong, H.K. / Mushtaq, A.U. / Kim, H.Y. / Yeo, K.J. / Kim, E. / Lee, W.C. / Hwang, K.Y. / Cheong, C. / Jeon, Y.H.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)12,1882
Polymers12,1882
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-28 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.844, 30.844, 196.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 ...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: 6094.047 Da / Num. of mol.: 2 / Fragment: SARAH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q13188, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.92 Å3/Da / Density % sol: 35.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M NaCl, 8% polyethylene glycol (PEG) 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 108264 / Num. obs: 108103 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 65.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6 / Rsym value: 0.206 / % possible all: 68.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4OH8

4oh8


Resolution: 1.699→30.471 Å / SU ML: 0.17 / σ(F): 1.45 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 1063 10 %RANDOM
Rwork0.2346 ---
obs0.2383 10694 93.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→30.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 0 109 953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007852
X-RAY DIFFRACTIONf_angle_d1.091135
X-RAY DIFFRACTIONf_dihedral_angle_d14.284357
X-RAY DIFFRACTIONf_chiral_restr0.065122
X-RAY DIFFRACTIONf_plane_restr0.005151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6992-1.77650.2885950.2507855X-RAY DIFFRACTION70
1.7765-1.87010.28271170.25421062X-RAY DIFFRACTION86
1.8701-1.98730.32151310.27161179X-RAY DIFFRACTION94
1.9873-2.14070.29091380.24941237X-RAY DIFFRACTION100
2.1407-2.35610.28151410.24651274X-RAY DIFFRACTION100
2.3561-2.69680.31961420.24981273X-RAY DIFFRACTION100
2.6968-3.3970.2831470.23611319X-RAY DIFFRACTION100
3.397-30.47550.2331580.21151426X-RAY DIFFRACTION100

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