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- PDB-5jqa: CaM:RM20 complex -

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Basic information

Entry
Database: PDB / ID: 5jqa
TitleCaM:RM20 complex
Components
  • Calmodulin
  • Myosin light chain kinase, smooth muscle
KeywordsCALCIUM BINDING PROTEIN/PROTEIN BINDING / calmodulin / calcium signal transduction / protein kinase / myosin light chain kinase / CALCIUM BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


aorta smooth muscle tissue morphogenesis / tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / cellular hypotonic response / : / establishment of protein localization to mitochondrial membrane / bleb assembly / type 3 metabotropic glutamate receptor binding / positive regulation of calcium ion transport ...aorta smooth muscle tissue morphogenesis / tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / cellular hypotonic response / : / establishment of protein localization to mitochondrial membrane / bleb assembly / type 3 metabotropic glutamate receptor binding / positive regulation of calcium ion transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / Calmodulin induced events / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / organelle localization by membrane tethering / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Glycogen breakdown (glycogenolysis) / regulation of synaptic vesicle exocytosis / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / response to corticosterone / positive regulation of wound healing / activation of adenylate cyclase activity / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / nitric-oxide synthase binding / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase activator activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / cleavage furrow / : / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / regulation of cardiac muscle contraction / detection of calcium ion / smooth muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol 3-kinase binding / eNOS activation / Protein methylation / voltage-gated potassium channel complex / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / stress fiber / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / nitric-oxide synthase regulator activity / Ras activation upon Ca2+ influx through NMDA receptor / response to amphetamine / sarcomere / regulation of heart rate / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of nitric-oxide synthase activity / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / : / : / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type 3 domain ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / : / : / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type 3 domain / EF-hand domain pair / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III 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 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Myosin light chain kinase, smooth muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTokars, V.L. / Minasov, G. / Anderson, W.F. / Watterson, D.M.
CitationJournal: To be Published
Title: CaM:RM20 complex
Authors: Tokars, V.L. / Minasov, G. / Anderson, W.F. / Watterson, D.M.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Myosin light chain kinase, smooth muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3336
Polymers19,1722
Non-polymers1604
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-73 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.016, 57.048, 45.068
Angle α, β, γ (deg.)90.00, 98.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Myosin light chain kinase, smooth muscle / smMLCK / Kinase-related protein / KRP / Telokin


Mass: 2319.760 Da / Num. of mol.: 1 / Fragment: UNP residues 1691-1710 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15746
#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.: 155 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, pH 4.6, 25% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 15660 / % possible obs: 95.5 % / Redundancy: 96.6 % / Net I/σ(I): 14.1
Reflection shellHighest resolution: 1.72 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O5G

2o5g


Resolution: 1.8→28.72 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.796 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18845 658 4.9 %RANDOM
Rwork0.1534 ---
obs0.15515 12699 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.522 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.18 Å2
2---0.24 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 4 155 1482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191464
X-RAY DIFFRACTIONr_bond_other_d0.0010.021380
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9611971
X-RAY DIFFRACTIONr_angle_other_deg0.81933195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1615187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.06525.43281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64215293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7051512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.021725
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02327
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_it2.0871.866725
X-RAY DIFFRACTIONr_mcbond_other2.0751.857723
X-RAY DIFFRACTIONr_mcangle_it3.2572.758919
X-RAY DIFFRACTIONr_mcangle_other3.2572.763920
X-RAY DIFFRACTIONr_scbond_it2.7422.256739
X-RAY DIFFRACTIONr_scbond_other2.742.259740
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4813.2321053
X-RAY DIFFRACTIONr_long_range_B_refined7.06615.9471972
X-RAY DIFFRACTIONr_long_range_B_other7.00415.4781907
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
Rfree0.256 52 -
Rwork0.219 910 -
obs--97.07 %
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)
10.5434-0.33930.76990.4639-0.40131.1206-0.0695-0.0729-0.01080.05070.06990.0122-0.0978-0.0919-0.00030.01640.0255-0.00420.05190.00440.0371-6.92661.2518-7.7556
20.90140.0534-0.070.5276-0.12960.1594-0.0088-0.03680.0725-0.0134-0.0003-0.00780.0346-0.01340.00910.0167-0.0057-0.01260.0459-0.00340.0337-1.3731-17.5265-14.1849
32.8862-1.8709-1.60741.46570.68551.401-0.0578-0.01370.0596-0.00040.054-0.06990.0872-0.06580.00380.0113-0.0048-0.00910.0573-0.00780.0402-3.2795-7.374-7.1853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 77
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2A78 - 148
4X-RAY DIFFRACTION2A403 - 404
5X-RAY DIFFRACTION3B1 - 21

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