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- PDB-4oh8: Crystal Structure of the human MST1-RASSF5 SARAH heterodimer -

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Basic information

Entry
Database: PDB / ID: 4oh8
TitleCrystal Structure of the human MST1-RASSF5 SARAH heterodimer
Components
  • Ras association domain-containing protein 5
  • Serine/threonine-protein kinase 4Serine/threonine-specific protein kinase
Keywordstransferase/Apoptosis / Coiled-coil / SARAH domain / homodimerization / heterodomerization / transferase-Apoptosis complex
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 / negative regulation of lymphocyte proliferation / lymphocyte proliferation / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development ...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 / negative regulation of lymphocyte proliferation / lymphocyte proliferation / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling / regulation of protein localization to nucleus / 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 / positive regulation of protein ubiquitination / 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 peptidyl-serine phosphorylation / positive regulation of protein binding / peptidyl-serine phosphorylation / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / protein stabilization / nuclear body / 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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 ...Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53, subunit A / p53-like tetramerisation domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / p53-like tetramerisation domain superfamily / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Ubiquitin-like domain superfamily / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase 4 / Ras association domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.281 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 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 4
B: Ras association domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)12,6392
Polymers12,6392
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-20 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.940, 85.840, 92.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serine/threonine-protein kinase 4 / Serine/threonine-specific protein kinase / Mammalian STE20-like protein kinase 1 / MST-1 / STE20-like kinase MST1 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 1 / MST-1 / STE20-like kinase MST1 / Serine/threonine-protein kinase Krs-2 / Serine/threonine-protein kinase 4 37kDa subunit / MST1/N / Serine/threonine-protein kinase 4 18kDa subunit / MST1/C


Mass: 6119.969 Da / Num. of mol.: 1 / Fragment: MST1 SARAH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK4, KRS2, MST1 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q13043, non-specific serine/threonine protein kinase
#2: Protein Ras association domain-containing protein 5 / New ras effector 1 / Regulator for cell adhesion and polarization enriched in lymphoid tissues / RAPL


Mass: 6519.258 Da / Num. of mol.: 1 / Fragment: RASSF5 SARAH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASSF5, NORE1, RAPL / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8WWW0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 35% (v/v) 2-methyl-2,4-pentanediol (MPD) acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 23288 / Num. obs: 22807 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 31.733
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6.031 / Num. unique all: 23288 / Rsym value: 0.206 / % possible all: 85.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.281→25.093 Å / SU ML: 0.3 / σ(F): 1.38 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 242 4.59 %RANDOM
Rwork0.2167 ---
obs0.2195 5278 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.281→25.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 0 22 784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008774
X-RAY DIFFRACTIONf_angle_d1.1221037
X-RAY DIFFRACTIONf_dihedral_angle_d16.27316
X-RAY DIFFRACTIONf_chiral_restr0.079111
X-RAY DIFFRACTIONf_plane_restr0.004136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2805-2.87260.31891160.21392439X-RAY DIFFRACTION97
2.8726-25.09460.26481260.21772597X-RAY DIFFRACTION99

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