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- PDB-5jth: Crystal structure of E67A calmodulin - CaM:RM20 analog complex -

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Basic information

Entry
Database: PDB / ID: 5jth
TitleCrystal structure of E67A calmodulin - CaM:RM20 analog complex
Components
  • Calmodulin
  • Myosin light chain kinase, smooth muscle
KeywordsTRANSFERASE / E67A calmodulin / calcium signal transduction / protein kinase / myosin light chain kinase
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 ...aorta smooth muscle tissue morphogenesis / tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / : / : / : / : / : / cellular hypotonic response / positive regulation of protein autophosphorylation / bleb assembly / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / positive regulation of calcium ion transport / type 3 metabotropic glutamate receptor binding / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / 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 / response to corticosterone / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / positive regulation of wound healing / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / cleavage furrow / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / smooth muscle contraction / Regulation of MECP2 expression and activity / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / Protein methylation / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / stress fiber / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / enzyme regulator activity / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to amphetamine / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation
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 / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...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 / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / EF-hand domain pair / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / 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 / Resolution: 1.84 Å
AuthorsGrum-Tokars, V.L. / Minasov, G. / Anderson, W.F. / Watterson, D.M.
CitationJournal: To Be Published
Title: Crystal structure of E67A calmodulin - CaM:RM20 analog complex
Authors: Grum-Tokars, V.L. / Minasov, G. / Anderson, W.F. / Watterson, D.M.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / struct / struct_conn / struct_conn_type
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,3016
Polymers19,1402
Non-polymers1604
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-74 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.094, 57.053, 44.871
Angle α, β, γ (deg.)90.00, 97.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin / CaM


Mass: 16794.510 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: 2345.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15746, myosin-light-chain 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.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 36.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium Acetate pH 4.6, 25%(w/v) PEG 4000, 20mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 12634 / % possible obs: 99.8 % / Redundancy: 7.2 % / Net I/σ(I): 31.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.84→28 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.958 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 614 4.9 %RANDOM
Rwork0.1567 ---
obs0.15877 12001 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-2.02 Å2
2---1.19 Å20 Å2
3---2.47 Å2
Refinement stepCycle: 1 / Resolution: 1.84→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 4 122 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191449
X-RAY DIFFRACTIONr_bond_other_d0.0010.021369
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.9561949
X-RAY DIFFRACTIONr_angle_other_deg1.02233177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9185185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.25225.5779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12915294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.111511
X-RAY DIFFRACTIONr_chiral_restr0.1350.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.021698
X-RAY DIFFRACTIONr_gen_planes_other0.020.02321
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_it2.0932.047717
X-RAY DIFFRACTIONr_mcbond_other2.0752.041715
X-RAY DIFFRACTIONr_mcangle_it3.2463.034909
X-RAY DIFFRACTIONr_mcangle_other3.2443.038910
X-RAY DIFFRACTIONr_scbond_it3.1942.461732
X-RAY DIFFRACTIONr_scbond_other3.1922.463733
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.093.5371041
X-RAY DIFFRACTIONr_long_range_B_refined7.88217.1941891
X-RAY DIFFRACTIONr_long_range_B_other7.79716.831852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 43 -
Rwork0.227 787 -
obs--89.63 %
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)
12.4328-0.70631.54631.4996-0.8112.367-0.1354-0.2860.03520.18220.12440.0536-0.1871-0.1840.01110.04070.03240.0270.0994-0.00020.043-7.19891.0428-7.5408
22.8085-0.2046-0.23512.6707-0.25581.2301-0.0312-0.10150.1450.04270.0388-0.0199-0.031-0.0127-0.00750.003-0.00420.00160.0762-0.02030.0173-1.7482-17.8031-14.1812
38.2298-4.3419-3.0454.57711.76383.45630.015-0.23360.14550.23260.157-0.2270.0272-0.0231-0.17190.0284-0.0063-0.01140.0575-0.01290.0259-3.5957-7.8235-6.8627
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 DIFFRACTION3B2 - 22

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