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- PDB-1zuz: Calmodulin in complex with a mutant peptide from human DRP-1 kinase -

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Basic information

Entry
Database: PDB / ID: 1zuz
TitleCalmodulin in complex with a mutant peptide from human DRP-1 kinase
Components
  • DRP-1 kinase
  • calmodulin
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / EF-hand / phosphorylation-mimicking point mutation / METAL BINDING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / : / : / 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 ...positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / : / : / 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 / Caspase activation via Dependence Receptors in the absence of ligand / anoikis / CaM pathway / Cam-PDE 1 activation / positive regulation of neutrophil chemotaxis / 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 / Calcineurin activates NFAT / protein phosphatase activator activity / Regulation of MECP2 expression and activity / regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase binding / 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 / 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 / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / 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 ...EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Death-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
DepositionJun 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 20, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_conn_angle / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 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: DRP-1 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5336
Polymers19,3732
Non-polymers1604
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-73 kcal/mol
Surface area8850 Å2
MethodPISA
2
A: calmodulin
B: DRP-1 kinase
hetero molecules

A: calmodulin
B: DRP-1 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,06612
Polymers38,7454
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7800 Å2
ΔGint-157 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.520, 34.030, 73.850
Angle α, β, γ (deg.)90.00, 109.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein calmodulin


Mass: 16965.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide DRP-1 kinase


Mass: 2406.855 Da / Num. of mol.: 1 / Mutation: S308D / Source method: obtained synthetically
Details: synthetic peptide, mutation S308D, the sequence of the peptide: calmodulin-binding domain is naturally found in Homo sapiens.
References: UniProt: Q9UIK4*PLUS
#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.: 121 / 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 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG3350, MPD, 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: X11 / Wavelength: 0.813 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 1.91→20 Å / Num. all: 12230 / Num. obs: 12230 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.044 / Net I/σ(I): 19.9
Reflection shellResolution: 1.91→2 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1542 / Rsym value: 0.332 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wrz

1wrz


Resolution: 1.91→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.885 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.192 / ESU R Free: 0.174 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24829 611 5 %RANDOM
Rwork0.19131 ---
all0.1941 12222 --
obs0.1941 12222 99.29 %-
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: 38.722 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.15 Å2
2---0.32 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.91→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 4 121 1437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221398
X-RAY DIFFRACTIONr_bond_other_d0.0050.021236
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9581879
X-RAY DIFFRACTIONr_angle_other_deg0.79832890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2595175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84225.33375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70315268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4681510
X-RAY DIFFRACTIONr_chiral_restr0.070.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
X-RAY DIFFRACTIONr_nbd_refined0.2310.2396
X-RAY DIFFRACTIONr_nbd_other0.170.21267
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2715
X-RAY DIFFRACTIONr_nbtor_other0.0850.2719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.292
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.214
X-RAY DIFFRACTIONr_mcbond_it1.3032892
X-RAY DIFFRACTIONr_mcbond_other0.232355
X-RAY DIFFRACTIONr_mcangle_it1.75431377
X-RAY DIFFRACTIONr_scbond_it2.2664577
X-RAY DIFFRACTIONr_scangle_it3.2655502
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 43 -
Rwork0.245 825 -
obs--95.38 %
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)
16.6311-2.41190.57263.2303-0.29952.19530.09110.2534-0.2002-0.2109-0.04940.22470.1467-0.0183-0.0416-0.24960.0154-0.009-0.1932-0.0175-0.16112.59686.008327.2786
21.9608-0.8963-1.64249.76993.08410.10710.0679-0.2890.065-0.1327-0.0695-0.14090.58080.18240.00160.22940.0095-0.0654-0.0517-0.0041-0.173715.4176-6.50429.5833
319.3985-13.5709-6.865217.51679.069213.8322-0.3829-0.7364-0.07490.3080.5349-0.17750.66330.8754-0.152-0.0372-0.0178-0.048-0.056-0.0172-0.139113.4714-2.771920.2813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 785 - 79
2X-RAY DIFFRACTION2AA79 - 14880 - 149
3X-RAY DIFFRACTION3BB302 - 3201 - 19

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