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- PDB-2jo8: Solution structure of C-terminal domain of human mammalian steril... -

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Basic information

Entry
Database: PDB / ID: 2jo8
TitleSolution structure of C-terminal domain of human mammalian sterile 20-like kinase 1 (MST1)
ComponentsSerine/threonine-protein kinase 4
KeywordsTRANSFERASE / protein / c-terminal domain / human mammalian sterile 20-like kinase 1 / dimer
Function / homology
Function and homology information


positive regulation of hepatocyte apoptotic process / 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 / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling ...positive regulation of hepatocyte apoptotic process / 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 / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / organ growth / branching involved in blood vessel morphogenesis / 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 / keratinocyte differentiation / protein serine/threonine kinase activator activity / epithelial cell proliferation / central nervous system development / protein tetramerization / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of peptidyl-serine phosphorylation / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / nuclear body / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / magnesium ion binding / signal transduction / protein homodimerization activity / protein-containing complex / nucleoplasm / 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, 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHwang, E. / Ryu, K.-S. / Paakkonen, K. / Guntert, P. / Cheong, H.-K. / Lim, D.-S. / Lee, J.O. / Jeon, Y.H. / Cheong, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insight into dimeric interaction of the SARAH domains from Mst1 and RASSF family proteins in the apoptosis pathway
Authors: Hwang, E. / Ryu, K.-S. / Paakkonen, K. / Guntert, P. / Cheong, H.-K. / Lim, D.-S. / Lee, J.-O. / Jeon, Y.H. / Cheong, C.
History
DepositionFeb 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 4
B: Serine/threonine-protein kinase 4


Theoretical massNumber of molelcules
Total (without water)12,2402
Polymers12,2402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine/threonine-protein kinase 4 / STE20-like kinase MST1 / MST-1 / Mammalian STE20-like protein kinase 1 / Serine/threonine-protein kinase Krs-2


Mass: 6119.969 Da / Num. of mol.: 2
Fragment: C-terminal SARAH domain, database residues 432-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK4, MST1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q13043, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D CBCANH
1313D HN(CA)CO
1413D HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D C(CCO)NH
1913D (H)CCH-COSY
11013D CCH-TOCSY
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11412D 1H-15N HSQC
11512D 1H-13C HSQC
11613D filter-edited 1H-15N NOESY
11713D filter-edited 1H-13C NOESY
11812D IPAP-1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] c-terminal domain of Mammalian sterile 20-like kinase 1, 100 mM sodium chloride, 2 mM DTT, 25 mM HEPES, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMc-terminal domain of Mammalian sterile 20-like kinase 1[U-13C; U-15N]1
100 mMsodium chloride1
2 mMDTT1
25 mMHEPES1
Sample conditionsIonic strength: 125 / pH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002
Bruker Avance IIBrukerAVANCE II9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.chemical shift assignment
CYANA2.1P.GUNTERT ET AL.structure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
TALOSCornilescu, Delaglio and Baxdihedral angle restraints
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1751 / NOE intraresidue total count: 144 / NOE long range total count: 160 / NOE medium range total count: 360 / NOE sequential total count: 1077 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 41
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 2 Å

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