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- PDB-3ujg: Crystal structure of SnRK2.6 in complex with HAB1 -

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Basic information

Entry
Database: PDB / ID: 3ujg
TitleCrystal structure of SnRK2.6 in complex with HAB1
Components
  • Protein phosphatase 2C 16
  • Serine/threonine-protein kinase SRK2E
KeywordsSIGNALING PROTEIN / SnRK2.6 / kinase / protein phosphatase 2C / ABA signaling
Function / homology
Function and homology information


cellular response to absence of light / regulation of anion channel activity / regulation of stomatal opening / triglyceride biosynthetic process / unsaturated fatty acid biosynthetic process / positive regulation of abscisic acid-activated signaling pathway / cellular response to carbon dioxide / sucrose metabolic process / regulation of stomatal closure / stomatal movement ...cellular response to absence of light / regulation of anion channel activity / regulation of stomatal opening / triglyceride biosynthetic process / unsaturated fatty acid biosynthetic process / positive regulation of abscisic acid-activated signaling pathway / cellular response to carbon dioxide / sucrose metabolic process / regulation of stomatal closure / stomatal movement / calcium-dependent protein serine/threonine kinase activity / leaf development / regulation of stomatal movement / response to abscisic acid / response to water deprivation / abscisic acid-activated signaling pathway / regulation of reactive oxygen species metabolic process / response to osmotic stress / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / response to salt stress / kinase activity / protein autophosphorylation / protein phosphatase 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 / defense response to bacterium / protein serine kinase activity / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
Serine/threonine-protein kinase SRK2E / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsZhou, X.E. / Soon, F.-F. / Ng, L.-M. / Kovach, A. / Tan, M.H.E. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Brunzelle, J.S. / Li, J. ...Zhou, X.E. / Soon, F.-F. / Ng, L.-M. / Kovach, A. / Tan, M.H.E. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Brunzelle, J.S. / Li, J. / Melcher, K. / Xu, H.E.
CitationJournal: Science / Year: 2012
Title: Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases.
Authors: Soon, F.F. / Ng, L.M. / Zhou, X.E. / West, G.M. / Kovach, A. / Tan, M.H. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Chalmers, M.J. / Brunzelle, J.S. / Zhang, H. / Yang, H. / Jiang, H. / Li, J. ...Authors: Soon, F.F. / Ng, L.M. / Zhou, X.E. / West, G.M. / Kovach, A. / Tan, M.H. / Suino-Powell, K.M. / He, Y. / Xu, Y. / Chalmers, M.J. / Brunzelle, J.S. / Zhang, H. / Yang, H. / Jiang, H. / Li, J. / Yong, E.L. / Cutler, S. / Zhu, J.K. / Griffin, P.R. / Melcher, K. / Xu, H.E.
History
DepositionNov 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase SRK2E
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8627
Polymers79,5252
Non-polymers3375
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-82 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.835, 154.835, 70.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Serine/threonine-protein kinase SRK2E / Protein OPEN STOMATA 1 / SNF1-related kinase 2.6 / SnRK2.6 / Serine/threonine-protein kinase OST1


Mass: 41053.453 Da / Num. of mol.: 1 / Fragment: Kinase domain / Mutation: D296A, E297A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SRK2E, OST1, SNRK2.6, At4g33950, F17I5.140 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q940H6, non-specific serine/threonine protein kinase
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 38471.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 1.2 M ammonium sulphate, 2% (w/v) PEG 1000, 3% (w/v) trimethylamine N-oxide dihydrate, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2010
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 26409 / % possible obs: 83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.4 Å11.98 Å
Translation3.4 Å11.98 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHASER1.3.2phasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.21 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1878 7.2 %RANDOM
Rwork0.207 ---
all0.2092 ---
obs0.2092 26402 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 107.44 Å2 / Biso mean: 56.278 Å2 / Biso min: 23.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2--2.4 Å20 Å2
3----4.81 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 17 146 4941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224884
X-RAY DIFFRACTIONr_bond_other_d0.0020.023379
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9636592
X-RAY DIFFRACTIONr_angle_other_deg0.8638209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79823.556225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05615865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0051539
X-RAY DIFFRACTIONr_chiral_restr0.070.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02986
X-RAY DIFFRACTIONr_mcbond_it0.7871.53006
X-RAY DIFFRACTIONr_mcbond_other0.0841.51220
X-RAY DIFFRACTIONr_mcangle_it1.4824848
X-RAY DIFFRACTIONr_scbond_it1.50331878
X-RAY DIFFRACTIONr_scangle_it2.6374.51744
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 148 -
Rwork0.32 1769 -
all-1917 -
obs--99.79 %

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