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- PDB-2y4v: CRYSTAL STRUCTURE OF HUMAN CALMODULIN IN COMPLEX WITH A DAP KINAS... -

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Basic information

Entry
Database: PDB / ID: 2y4v
TitleCRYSTAL STRUCTURE OF HUMAN CALMODULIN IN COMPLEX WITH A DAP KINASE-1 MUTANT (W305Y) PEPTIDE
Components
  • CALMODULIN
  • DEATH-ASSOCIATED PROTEIN KINASE 1,
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / 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 / : / establishment of protein localization to mitochondrial membrane / 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 ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / 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 / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / syntaxin-1 binding / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / calmodulin-dependent protein kinase activity / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / positive regulation of cyclic-nucleotide phosphodiesterase activity / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / adenylate cyclase binding / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / extrinsic apoptotic signaling pathway via death domain receptors / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / calcium channel inhibitor activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Ion homeostasis / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated potassium channel complex / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / positive regulation of nitric-oxide synthase activity
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / 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 ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / 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 / Ankyrin repeat-containing domain superfamily / EF-hand, calcium binding motif / 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
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: 1.8 Å
Authorsde Diego, I. / Lehmann, F. / Wilmanns, M.
CitationJournal: To be Published
Title: A Journey Through the Dap Kinase Architecture
Authors: De Diego, I. / Kuper, J. / Lehmann, F. / Wilmanns, M.
History
DepositionJan 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 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: CALMODULIN
B: DEATH-ASSOCIATED PROTEIN KINASE 1,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3836
Polymers19,2222
Non-polymers1604
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-75.9 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.561, 33.923, 74.257
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2146-

HOH

21A-2149-

HOH

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Components

#1: Protein CALMODULIN


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide DEATH-ASSOCIATED PROTEIN KINASE 1, / DAP KINASE 1


Mass: 2369.899 Da / Num. of mol.: 1 / Fragment: RESIDUES 302-320 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#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.: 165 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, TRP 305 TO TYR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.73 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 25(W/V) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99989
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2009 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.8→23.59 Å / Num. obs: 14844 / % possible obs: 96.9 % / Observed criterion σ(I): 3.3 / Redundancy: 1.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.3 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YR5

1yr5


Resolution: 1.8→74.2 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.055 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1A-3A AND 78A-80A ARE DISORDERED AND REMOVED FROM MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.23825 743 5 %RANDOM
Rwork0.22908 ---
obs0.22954 14099 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.612 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å2-0.9 Å2
2--0.16 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→74.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 4 165 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221211
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9691627
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40126.03458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26415217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.458156
X-RAY DIFFRACTIONr_chiral_restr0.1330.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02906
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3461.5781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35921240
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0183430
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.914.5387
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 62 -
Rwork0.298 1040 -
obs--95.99 %
Refinement TLS params.Method: refined / Origin x: 4.6527 Å / Origin y: -1.2498 Å / Origin z: 20.7359 Å
111213212223313233
T0.0084 Å20.0305 Å20.0053 Å2-0.0268 Å20.0019 Å2--0.0289 Å2
L-0.2114 °20.102 °20.2464 °2-0.1505 °20.0238 °2--0.6924 °2
S-0.0158 Å °-0.0377 Å °-0.0388 Å °-0.0471 Å °0.0346 Å °0.0277 Å °-0.0197 Å °0.0412 Å °-0.0188 Å °

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