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- PDB-2ehb: The structure of the C-terminal domain of the protein kinase AtSO... -

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Basic information

Entry
Database: PDB / ID: 2ehb
TitleThe structure of the C-terminal domain of the protein kinase AtSOS2 bound to the calcium sensor AtSOS3
Components
  • CBL-interacting serine/threonine-protein kinase 24
  • Calcineurin B-like protein 4
KeywordsSIGNALLING PROTEIN/Transferase / protein complex / Ca(II) ions bound to SOS3 (EF-hands 1 and 4) / SOS2 FISL motif / SOS2 phosphatase binding domain (PPI) / SIGNALLING PROTEIN-Transferase COMPLEX
Function / homology
Function and homology information


hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / plant-type vacuole membrane / calcineurin complex / intracellular potassium ion homeostasis / detection of calcium ion / response to salt stress / calcium-mediated signaling / kinase binding / eukaryotic translation initiation factor 2alpha kinase activity ...hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / plant-type vacuole membrane / calcineurin complex / intracellular potassium ion homeostasis / detection of calcium ion / response to salt stress / calcium-mediated signaling / kinase binding / 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 / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / calcium ion binding / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
NAF domain / NAF/FISL domain / NAF domain / NAF domain profile. / Calcineurin B-like / Kinase associated domain 1, KA1 / EF hand / TATA-Binding Protein / EF-hand / Recoverin; domain 1 ...NAF domain / NAF/FISL domain / NAF domain / NAF domain profile. / Calcineurin B-like / Kinase associated domain 1, KA1 / EF hand / TATA-Binding Protein / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Calcineurin B-like protein 4 / CBL-interacting serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSanchez-Barrena, M.J.
CitationJournal: Mol.Cell / Year: 2007
Title: The structure of the C-terminal domain of the protein kinase AtSOS2 bound to the calcium sensor AtSOS3
Authors: Sanchez-Barrena, M.J. / Fujii, H. / Angulo, I. / Martinez-Ripoll, M. / Zhu, J.K. / Albert, A.
History
DepositionMar 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcineurin B-like protein 4
D: CBL-interacting serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4954
Polymers40,4152
Non-polymers802
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-44 kcal/mol
Surface area15510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.137, 57.387, 141.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calcineurin B-like protein 4 / Protein SALT OVERLY SENSITIVE 3 / SOS3


Mass: 24045.750 Da / Num. of mol.: 1 / Fragment: residues in database 1-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOS3 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3) / References: UniProt: O81223
#2: Protein CBL-interacting serine/threonine-protein kinase 24 / SALT OVERLY SENSITIVE 2 protein / SOS2 / SNF1-related kinase 3.11


Mass: 16368.982 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 304-446)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOS2 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)
References: UniProt: Q9LDI3, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: drops: 10mg/ml SOS3:C-SOS2, reservoir solution: 20%(w/v) PEG4000, 0.1M Tris-HCl pH 7.5, 0.2M Lithium Sulfate, 3%(v/v) Ethylene Glycol; 1M Guanidine HCl in a ratio of 1:1:0.5, VAPOR ...Details: drops: 10mg/ml SOS3:C-SOS2, reservoir solution: 20%(w/v) PEG4000, 0.1M Tris-HCl pH 7.5, 0.2M Lithium Sulfate, 3%(v/v) Ethylene Glycol; 1M Guanidine HCl in a ratio of 1:1:0.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2006
Details: The main optical elements are a liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror, the latter which is bent to approximate to a toroidal curvature.
RadiationMonochromator: There is a high resolution Si(311) cut and a lower resolution Si(111) cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→70.9 Å / Num. all: 25141 / Num. obs: 25141 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.35 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of SOS3

Resolution: 2.1→70.89 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.57 / SU ML: 0.17 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.242 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25932 1066 4.9 %RANDOM
Rwork0.21453 ---
all0.2168 20664 --
obs0.2168 20664 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.969 Å2
Baniso -1Baniso -2Baniso -3
1-4.88 Å20 Å20 Å2
2---2.42 Å20 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 2 210 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222556
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9673437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48923.73126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57415486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5281521
X-RAY DIFFRACTIONr_chiral_restr0.0960.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021902
X-RAY DIFFRACTIONr_nbd_refined0.2340.21189
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2184
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.214
X-RAY DIFFRACTIONr_mcbond_it0.8431.51587
X-RAY DIFFRACTIONr_mcangle_it1.42222484
X-RAY DIFFRACTIONr_scbond_it2.19331084
X-RAY DIFFRACTIONr_scangle_it3.634.5953
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 78 -
Rwork0.286 1488 -
obs-1488 99.18 %

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