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- PDB-2x0g: X-RAY STRUCTURE OF A DAP-KINASE CALMODULIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2x0g
TitleX-RAY STRUCTURE OF A DAP-KINASE CALMODULIN COMPLEX
Components
  • CALMODULIN
  • DEATH-ASSOCIATED PROTEIN KINASE 1
KeywordsTRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / TRANSFERASE SIGNALING PROTEIN COMPLEX / PHOSPHOPROTEIN / CALMODULIN-BINDING / DAPK / KINASE / ANK REPEAT / CALMODULIN / TRANSFERASE / ATP-BINDING
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / : / positive regulation of protein autophosphorylation ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / Caspase activation via Dependence Receptors in the absence of ligand / defense response to tumor cell / type 3 metabotropic glutamate receptor binding / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / Reduction of cytosolic Ca++ levels / syntaxin-1 binding / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / extrinsic apoptotic signaling pathway via death domain receptors / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / activation of adenylate cyclase activity / Protein methylation / calcium channel inhibitor activity / presynaptic cytosol / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / positive regulation of nitric-oxide synthase activity / titin binding / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / positive regulation of autophagy / substantia nigra development / FCERI mediated Ca+2 mobilization / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / nitric-oxide synthase regulator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / sarcomere
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calmodulin-1 / Death-associated protein kinase 1 / Calmodulin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKuper, J. / De Diego, I. / Lehmann, F. / Wilmanns, M.
CitationJournal: Sci.Signal / Year: 2010
Title: Molecular Basis of the Death-Associated Protein Kinase-Calcium/Calmodulin Regulator Complex.
Authors: De Diego, I. / Kuper, J. / Bakalova, N. / Kursula, P. / Wilmanns, M.
History
DepositionDec 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE 1
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5288
Polymers55,1752
Non-polymers3526
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-105.8 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.413, 101.694, 104.775
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 DEATH-ASSOCIATED PROTEIN KINASE 1 / DAP KINASE 1


Mass: 38454.086 Da / Num. of mol.: 1
Fragment: CATALYTIC AND AUTOINHIBITORY DOMAIN, RESIDUES 1- 334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM8A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.43 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 7.2
Details: 0.17M AMMONIUM SULFATE, 25% (W/V) PEG 4000, 15% GLYCEROL, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.277
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.277 Å / Relative weight: 1
ReflectionResolution: 2.2→72.93 Å / Num. obs: 25927 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JKS

1jks


Resolution: 2.2→52.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / SU B: 13.993 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1293 5 %RANDOM
Rwork0.201 ---
obs0.204 24589 99.8 %-
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: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20 Å2
2---2.32 Å2-0 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→52.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 14 177 3811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223700
X-RAY DIFFRACTIONr_bond_other_d0.0010.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9684984
X-RAY DIFFRACTIONr_angle_other_deg0.87336241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26425.132189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00415695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5631522
X-RAY DIFFRACTIONr_chiral_restr0.080.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02731
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.30332240
X-RAY DIFFRACTIONr_mcbond_other0.8213913
X-RAY DIFFRACTIONr_mcangle_it3.46543616
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.30161460
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.06781366
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 95 -
Rwork0.242 1777 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2370.70590.67756.8633-1.53541.8996-0.0740.72880.3775-0.2672-0.10720.1591-0.21040.17710.18110.06210.0056-0.04580.18380.01510.0656-3.25934.944-15.155
23.8525-0.3487-0.64763.66531.50113.1902-0.17790.2636-0.3544-0.108-0.15670.28940.5291-0.24140.33470.1542-0.06650.07570.0906-0.06740.1124-14.3479.467-15.41
319.4413-14.0814.739613.6547-9.241411.7909-0.3619-1.1365-1.1213-0.34821.20480.9786-0.5958-0.793-0.84290.60390.1180.12630.55270.27040.7502-3.97218.731-37.78
41.8802-0.414-1.18974.55980.57996.2878-0.23160.0971-0.5483-0.4751-0.07230.41470.7017-0.40230.3040.7792-0.10670.1050.3789-0.03550.6617-2.30433.804-41.621
55.99370.7893-0.58.70733.782611.92450.05240.24950.7997-0.87240.14820.0999-1.00340.0122-0.20060.2873-0.03070.07280.1618-0.03170.24525.68610.367-35.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 91
2X-RAY DIFFRACTION1A1321
3X-RAY DIFFRACTION2A96 - 303
4X-RAY DIFFRACTION2A1322
5X-RAY DIFFRACTION3A305 - 320
6X-RAY DIFFRACTION4B6 - 73
7X-RAY DIFFRACTION4B1148 - 1149
8X-RAY DIFFRACTION5B82 - 144
9X-RAY DIFFRACTION5B1146 - 1147

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