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- PDB-7psz: Crystal structure of CaM in complex with CDZ (form 1) -

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Basic information

Entry
Database: PDB / ID: 7psz
TitleCrystal structure of CaM in complex with CDZ (form 1)
ComponentsCalmodulin-1
KeywordsMETAL BINDING PROTEIN / Calmodulin / CDZ
Function / homology
Function and homology information


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 ...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 / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / 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 / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway
Similarity search - Function
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
Similarity search - Domain/homology
Chem-85H / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsMechaly, A.E. / Leger, C. / Haouz, A. / Chenal, A.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Bmc Biol. / Year: 2022
Title: Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium.
Authors: Leger, C. / Pitard, I. / Sadi, M. / Carvalho, N. / Brier, S. / Mechaly, A. / Raoux-Barbot, D. / Davi, M. / Hoos, S. / Weber, P. / Vachette, P. / Durand, D. / Haouz, A. / Guijarro, J.I. / Ladant, D. / Chenal, A.
History
DepositionSep 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6307
Polymers16,7211
Non-polymers9096
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-58 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.848, 36.127, 68.382
Angle α, β, γ (deg.)90, 116.74, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

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Components

#1: Protein Calmodulin-1 /


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Chemical ChemComp-85H / 1-[bis(4-chlorophenyl)methyl]-3-[(2~{R})-2-(2,4-dichlorophenyl)-2-[(2,4-dichlorophenyl)methoxy]ethyl]imidazole


Mass: 652.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H23Cl6N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 30 %w/v PEG 8K and 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.898→33.392 Å / Num. obs: 11459 / % possible obs: 97.6 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Net I/σ(I): 15.6
Reflection shellResolution: 1.898→1.93 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 555 / CC1/2: 0.819 / Rpim(I) all: 0.359 / Rrim(I) all: 0.969 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CTR

1ctr


Resolution: 1.898→33.39 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 585 -RANDOM
Rwork0.2225 ---
obs0.2241 11459 97.6 %-
Displacement parametersBiso mean: 45.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.6434 Å20 Å21.5284 Å2
2---4.9468 Å20 Å2
3---2.3035 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.898→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 49 41 1236
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081210HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.831630HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d447SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes254HARMONIC5
X-RAY DIFFRACTIONt_it1210HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion155SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1052SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.29
X-RAY DIFFRACTIONt_other_torsion17.33
LS refinement shellResolution: 1.9→1.92 Å
RfactorNum. reflection% reflection
Rfree0.3278 14 -
Rwork0.2032 --
obs0.2075 396 97.03 %
Refinement TLS params.Origin x: -6.8959 Å / Origin y: 0.6511 Å / Origin z: 15.0079 Å
111213212223313233
T-0.0884 Å2-0.0221 Å20.0229 Å2--0.0463 Å2-0.0069 Å2---0.0099 Å2
L1.2416 °20.6299 °20.3575 °2-1.4278 °2-0.2737 °2--1.6701 °2
S-0.0456 Å °0.2193 Å °-0.0358 Å °0.2193 Å °0.007 Å °-0.059 Å °-0.0358 Å °-0.059 Å °0.0386 Å °
Refinement TLS groupSelection details: { A|* }

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