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- PDB-1yr5: 1.7-A structure of calmodulin bound to a peptide from DAP kinase -

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Basic information

Entry
Database: PDB / ID: 1yr5
Title1.7-A structure of calmodulin bound to a peptide from DAP kinase
Components
  • 19-mer from Death-associated protein kinase 1
  • calmodulin
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / EF hand / METAL BINDING PROTEIN-TRANSFERASE COMPLEX
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 / : / establishment of protein localization to mitochondrial membrane / negative regulation of peptidyl-threonine phosphorylation ...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 / : / establishment of protein localization to mitochondrial membrane / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / syntaxin-1 binding / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / extrinsic apoptotic signaling pathway via death domain receptors / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / positive regulation of autophagy / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / FCERI mediated Ca+2 mobilization / response to amphetamine / positive regulation of nitric-oxide synthase activity / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity
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 / EF-hand / : ...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 / EF-hand / : / Death-like domain superfamily / Recoverin; domain 1 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
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: 1.7 Å
AuthorsKursula, P. / Vahokoski, J. / Wilmanns, M.
CitationJournal: To be Published
Title: Recognition of human death-associated protein kinases by calmodulin
Authors: Kursula, P. / Vahokoski, J. / Wilmanns, M.
History
DepositionFeb 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_conn_angle / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: calmodulin
B: 19-mer from Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2756
Polymers19,1142
Non-polymers1604
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-68 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.070, 33.710, 75.890
Angle α, β, γ (deg.)90.00, 111.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein calmodulin


Mass: 16721.350 Da / Num. of mol.: 1 / Fragment: residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET8c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide 19-mer from Death-associated protein kinase 1 / DAP kinase 1


Mass: 2392.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P53355, EC: 2.7.1.37
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 8000, sodium acetate, calcium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.938 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.938 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 16769 / Num. obs: 16769 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.056 / Net I/σ(I): 20.1
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1362 / Rsym value: 0.52 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRZ

1wrz


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.353 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS PARAMETERS USED / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.143 / ESU R Free: 0.143 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25707 846 5 %RANDOM
Rwork0.19999 ---
all0.20286 16768 --
obs0.20286 16768 96.21 %-
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: 9.375 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20.81 Å2
2---0.87 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 4 144 1468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221497
X-RAY DIFFRACTIONr_bond_other_d0.0020.021299
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9611998
X-RAY DIFFRACTIONr_angle_other_deg2.02633049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49525.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41815289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5571510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021721
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02299
X-RAY DIFFRACTIONr_nbd_refined0.2290.2440
X-RAY DIFFRACTIONr_nbd_other0.2050.21382
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2774
X-RAY DIFFRACTIONr_nbtor_other0.0820.2816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.223
X-RAY DIFFRACTIONr_mcbond_it1.4082965
X-RAY DIFFRACTIONr_mcbond_other0.1652371
X-RAY DIFFRACTIONr_mcangle_it1.79731459
X-RAY DIFFRACTIONr_scbond_it2.5474.5622
X-RAY DIFFRACTIONr_scangle_it3.5966539
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 66 -
Rwork0.307 1149 -
obs--94.7 %
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)
16.6884-2.1573-0.47222.1704-1.04912.70280.11870.405-0.2559-0.2696-0.0490.11380.20690.0072-0.0697-0.20530.0414-0.0555-0.13590.0088-0.132511.26485.574628.048
23.7185-1.9325-1.38719.2413-0.346611.8097-0.2478-0.21370.14210.36880.1949-0.124-0.24520.09950.05290.0726-0.0135-0.0302-0.1617-0.0085-0.184614.9383-6.12539.2604
35.3771-5.3033-7.586613.66548.305714.7942-0.1595-0.788-0.0910.37930.12760.15060.47110.56780.03190.14830.0103-0.0444-0.0849-0.0116-0.133711.7032-2.895520.6681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 803 - 80
2X-RAY DIFFRACTION1AC - D151 - 1521
3X-RAY DIFFRACTION2AA81 - 14881 - 148
4X-RAY DIFFRACTION2AE - F153 - 1541
5X-RAY DIFFRACTION3BB302 - 3201 - 19

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