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- PDB-3o78: The structure of Ca2+ Sensor (Case-12) -

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Basic information

Entry
Database: PDB / ID: 3o78
TitleThe structure of Ca2+ Sensor (Case-12)
ComponentsMyosin light chain kinase, smooth muscle,Green fluorescent protein,Green fluorescent protein,Calmodulin-1
KeywordsFLUORESCENT PROTEIN / circular permutated green fluorescent protein / genetically encoded / GFP Calmodulin M13-peptide / Calcium sensor / M13-peptide / GYG naturally modified tripeptide acts as chromophore
Function / homology
Function and homology information


tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / CaM pathway / Cam-PDE 1 activation / 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 ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / CaM pathway / Cam-PDE 1 activation / 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 / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / 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 / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / cleavage furrow / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / 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 / stress fiber / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / 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 / FCERI mediated Ca+2 mobilization / 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 / bioluminescence / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / generation of precursor metabolites and energy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / lamellipodium / myelin sheath
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Green Fluorescent Protein / Green fluorescent protein / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / : / Green fluorescent protein, GFP / Recoverin; domain 1 ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Green Fluorescent Protein / Green fluorescent protein / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / : / Green fluorescent protein, GFP / Recoverin; domain 1 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Myosin light chain kinase, smooth muscle / Green fluorescent protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
Aequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLeder, L. / Stark, W. / Freuler, F. / Marsh, M. / Meyerhofer, M. / Stettler, T. / Mayr, L.M. / Britanova, O.V. / Strukova, L.A. / Chudakov, D.M.
CitationJournal: Sensors (Basel) / Year: 2010
Title: The structure of Ca2+ sensor Case16 reveals the mechanism of reaction to low Ca2+ concentrations
Authors: Leder, L. / Stark, W. / Freuler, F. / Marsh, M. / Meyerhofer, M. / Stettler, T. / Mayr, L.M. / Britanova, O.V. / Strukova, L.A. / Chudakov, D.M. / Souslova, E.A.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Jun 13, 2012Group: Database references
Revision 1.4Jun 21, 2017Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / diffrn_source ...diffrn_radiation_wavelength / diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list ..._diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _pdbx_entry_details.sequence_details / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_pdb_strand_id
Revision 1.5Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin light chain kinase, smooth muscle,Green fluorescent protein,Green fluorescent protein,Calmodulin-1
B: Myosin light chain kinase, smooth muscle,Green fluorescent protein,Green fluorescent protein,Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,30410
Polymers92,9842
Non-polymers3218
Water1,38777
1
A: Myosin light chain kinase, smooth muscle,Green fluorescent protein,Green fluorescent protein,Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6525
Polymers46,4921
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin light chain kinase, smooth muscle,Green fluorescent protein,Green fluorescent protein,Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6525
Polymers46,4921
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-46 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.374, 101.635, 82.211
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUARGARGAA25 - 27025 - 268
211LEULEUARGARGBB25 - 27025 - 268
112ASPASPMETMETAA271 - 340269 - 338
212ASPASPMETMETBB271 - 340269 - 338
113METMETVALVALAA341 - 411339 - 409
213METMETVALVALBB341 - 411339 - 409
123GLYGLYSERSERAA1 - 241 - 24
223GLYGLYSERSERBB1 - 241 - 24

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Myosin light chain kinase, smooth muscle,Green fluorescent protein,Green fluorescent protein,Calmodulin-1 / MLCK / Telokin


Mass: 46491.883 Da / Num. of mol.: 2 / Mutation: POINT MUTATIONS
Source method: isolated from a genetically manipulated source
Details: Chimera protein of peptide of M13 (residues 1730-1749, UNP P11799), C-terminal domain of Green fluorescent protein (residues 147-238, UNP P42212), linker, N-terminal of Green fluorescent ...Details: Chimera protein of peptide of M13 (residues 1730-1749, UNP P11799), C-terminal domain of Green fluorescent protein (residues 147-238, UNP P42212), linker, N-terminal of Green fluorescent protein (residues 2-146, UNP P42212) and residues 3-149 of Calmodulin (UNP P0DP23)
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: Mylk, GFP, CALM1, CALM, CAM, CAM1 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Tuner
References: UniProt: P11799, UniProt: P42212, UniProt: P0DP23, myosin-light-chain kinase
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsUNP RESIDUE 65 SER AND 72 SER OF GREEN FLUORESCENT PROTEIN IN DATABASE UNP P42212 (GFP_AEQVI) ...UNP RESIDUE 65 SER AND 72 SER OF GREEN FLUORESCENT PROTEIN IN DATABASE UNP P42212 (GFP_AEQVI) SHOULD BE GLY. RESIDUE S65G FORM THE CHROMOPHORE CR2 190. RESIDUE S72G (RESIDUE NUMBER 196 IN THE COORDINATES RESPECTIVELY) IS MUTAGENESIS. THESE SEQUENCE WERE BASED ON REFERENCES IN THE DATABASE UNP P42212.

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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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Reservoir: 100mM Tris HCL (pH 5.5), 100mM (NH4)2SO4, 21% PEG 3350; Protein stock: 7.6 mg/ml Protein, 50mM Tris HCl (pH 7.4), 150mM NaCl; Seed stock solution: 20mM CaCl2, 20% PEG 3350, VAPOR ...Details: Reservoir: 100mM Tris HCL (pH 5.5), 100mM (NH4)2SO4, 21% PEG 3350; Protein stock: 7.6 mg/ml Protein, 50mM Tris HCl (pH 7.4), 150mM NaCl; Seed stock solution: 20mM CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 23464 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 41.9 Å2 / Rsym value: 0.101 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.517 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O77

3o77


Resolution: 2.6→50.83 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.84 / SU B: 24.1 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31614 1173 5 %RANDOM
Rwork0.24183 ---
obs0.24546 22288 99.83 %-
all-22326 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.432 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20.06 Å2
2--0.32 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 8 77 6423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.9688674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3465795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78625.28322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.239151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6671534
X-RAY DIFFRACTIONr_chiral_restr0.1060.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.23511
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24392
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1780.225
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3720.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDNumberRms dev position (Å)
117930.07
25420.07
37540.09
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 85 -
Rwork0.34 1627 -
obs--99.77 %

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