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- PDB-1mxe: Structure of the Complex of Calmodulin with the Target Sequence o... -

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Basic information

Entry
Database: PDB / ID: 1mxe
TitleStructure of the Complex of Calmodulin with the Target Sequence of CaMKI
Components
  • Calmodulin
  • Target Sequence of rat Calmodulin-Dependent Protein Kinase I
KeywordsMETAL BINDING PROTEIN / Calmodulin-Pepide Complex / Calmodulin / CaMKI / XRAY
Function / homology
Function and homology information


Activation of RAC1 downstream of NMDARs / positive regulation of syncytium formation by plasma membrane fusion / metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development ...Activation of RAC1 downstream of NMDARs / positive regulation of syncytium formation by plasma membrane fusion / metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development / myosin V complex / : / kinetochore organization / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / : / actin filament-based movement / Ca2+/calmodulin-dependent protein kinase / rhodopsin mediated signaling pathway / Neutrophil degranulation / regulation of protein binding / myosin V binding / channel regulator activity / cellular response to ethanol / calmodulin-dependent protein kinase activity / nucleocytoplasmic transport / positive regulation of dendritic spine development / muscle cell cellular homeostasis / regulation of synapse organization / myosin heavy chain binding / positive regulation of muscle cell differentiation / mitotic spindle pole / centriole replication / enzyme regulator activity / centriole / positive regulation of protein export from nucleus / sensory perception of sound / positive regulation of protein serine/threonine kinase activity / positive regulation of neuron projection development / spindle / mitotic spindle / regulation of protein localization / sensory perception of smell / nervous system development / cell cortex / midbody / postsynaptic density / cell differentiation / calmodulin binding / intracellular signal transduction / cell cycle / protein phosphorylation / protein serine kinase activity / centrosome / glutamatergic synapse / calcium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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 / Serine/threonine-protein kinase, active site ...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 / Calcium/calmodulin-dependent protein kinase type 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsClapperton, J.A. / Martin, S.R. / Smerdon, S.J. / Gamblin, S.J. / Bayley, P.M.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of the Complex of Calmodulin with the Target Sequence of Calmodulin-Dependent Protein Kinase I: Studies of the Kinase Activation Mechanism
Authors: Clapperton, J.A. / Martin, S.R. / Smerdon, S.J. / Gamblin, S.J. / Bayley, P.M.
History
DepositionOct 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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_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
E: Target Sequence of rat Calmodulin-Dependent Protein Kinase I
B: Calmodulin
F: Target Sequence of rat Calmodulin-Dependent Protein Kinase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,70512
Polymers39,3844
Non-polymers3218
Water4,216234
1
A: Calmodulin
E: Target Sequence of rat Calmodulin-Dependent Protein Kinase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8526
Polymers19,6922
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-78 kcal/mol
Surface area9010 Å2
MethodPISA
2
B: Calmodulin
F: Target Sequence of rat Calmodulin-Dependent Protein Kinase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8526
Polymers19,6922
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-76 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.712, 69.581, 75.344
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 Calmodulin /


Mass: 16694.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62152
#2: Protein/peptide Target Sequence of rat Calmodulin-Dependent Protein Kinase I / CAM kinase I


Mass: 2997.628 Da / Num. of mol.: 2 / Fragment: Calmodulin Binding Domain / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: Q63450, EC: 2.7.1.123
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.11 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Cacodylate, Calcium chloride, MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 mg/mlprotein1drop
220 mMTris1droppH7.8
330 mM1dropNaCl
41 mM1dropCaCl2
550 mMsodium cacodylate1reservoirpH5.5
65 mM1reservoirCaCl2
753-60 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934, 0.9500, 0.9791, 0.9794
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.951
30.97911
40.97941
ReflectionResolution: 1.7→30 Å / Num. all: 39543 / Num. obs: 38674 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.217 / % possible all: 100
Reflection
*PLUS
Redundancy: 23.1 %
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.168 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22863 1982 5.1 %RANDOM
Rwork0.18791 ---
obs0.18998 36644 99.88 %-
all-39543 --
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 mean: 18.529 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2--3.54 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 8 234 2922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222714
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.953633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0533334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88815526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022057
X-RAY DIFFRACTIONr_nbd_refined0.2370.31361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.5193
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.534
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.386
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6540.531
X-RAY DIFFRACTIONr_mcbond_it1.0171.51672
X-RAY DIFFRACTIONr_mcangle_it1.77522679
X-RAY DIFFRACTIONr_scbond_it2.7931042
X-RAY DIFFRACTIONr_scangle_it4.3044.5954
X-RAY DIFFRACTIONr_rigid_bond_restr1.01322714
X-RAY DIFFRACTIONr_sphericity_free22.520244
X-RAY DIFFRACTIONr_sphericity_bonded5.771202682
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 134
Rwork0.21 2671
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)
12.356-0.8791-0.61662.54540.36222.7301-0.1064-0.0936-0.14550.23370.027-0.07960.180.03420.07940.1660.0173-0.00020.02640.07270.215334.5184.84112.426
24.7887-0.326-0.54151.8453-0.69452.80930.02260.26430.10520.1225-0.1062-0.0499-0.2443-0.0620.08360.15150.0244-0.00910.03360.03440.185624.34220.4961.874
32.1783-0.8166-2.00811.44911.00543.66280.12860.18690.0701-0.1467-0.06710.0574-0.1239-0.0913-0.06140.26490.0548-0.03480.0282-0.0140.153854.78653.0046.598
43.11230.42421.39313.44193.02476.7433-0.1508-0.1235-0.05170.04910.14130.07950.11860.40770.00940.15120.0569-0.00170.0864-0.00990.103270.10740.32917.271
54.1501-2.3501-1.9942.9281.69772.4404-0.0432-0.09260.08850.06750.0647-0.1127-0.02320.0814-0.02150.1972-0.0033-0.01760.02820.04040.198728.94416.0989.127
64.7447-3.5227-2.98494.05222.20962.52880.1199-0.07030.079-0.17820.0302-0.0459-0.19030.113-0.15010.1949-0.0142-0.02360.0965-0.02420.147665.70547.3199.948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 775 - 77
2X-RAY DIFFRACTION2AA78 - 14778 - 147
3X-RAY DIFFRACTION3BC5 - 775 - 77
4X-RAY DIFFRACTION4BC78 - 14778 - 147
5X-RAY DIFFRACTION5EB294 - 3181 - 25
6X-RAY DIFFRACTION6FD294 - 3181 - 25
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.205
LS refinement shell
*PLUS

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