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- PDB-7pu9: Crystal structure of CaM in complex with CDZ (form 2) -

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Basic information

Entry
Database: PDB / ID: 7pu9
TitleCrystal structure of CaM in complex with CDZ (form 2)
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 / 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 / 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 / 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 / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / 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 / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / centrosome
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 ...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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-85H / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.279 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 28, 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)18,1867
Polymers16,7211
Non-polymers1,4656
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-51 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.351, 39.351, 336.92
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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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.: 2 / Source method: obtained synthetically / Formula: C31H23Cl6N2O / Feature type: SUBJECT OF INVESTIGATION
#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.: 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.2 M CaCl2, 0.1 M Tris pH 8.5 and 25 %w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8266 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 2.279→56.153 Å / Num. obs: 8009 / % possible obs: 100 % / Redundancy: 34.8 % / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.027 / Rrim(I) all: 0.159 / Net I/σ(I): 14.9
Reflection shellResolution: 2.279→2.318 Å / Rmerge(I) obs: 2.112 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 395 / CC1/2: 0.882 / Rpim(I) all: 0.334 / Rrim(I) all: 2.139 / % possible all: 100

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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: 2.279→56.15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.344 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.238
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 406 -RANDOM
Rwork0.2341 ---
obs0.2358 8009 100 %-
Displacement parametersBiso mean: 60.49 Å2
Baniso -1Baniso -2Baniso -3
1--5.9822 Å20 Å20 Å2
2---5.9822 Å20 Å2
3---11.9645 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.279→56.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1134 0 84 41 1259
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081234HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.881663HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d447SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes290HARMONIC5
X-RAY DIFFRACTIONt_it1234HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion153SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1124SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion17.98
LS refinement shellResolution: 2.28→2.32 Å
RfactorNum. reflection% reflection
Rfree0.2 12 -
Rwork0.226 --
obs0.2251 401 100 %
Refinement TLS params.Origin x: -9.827 Å / Origin y: 16.9688 Å / Origin z: 12.4669 Å
111213212223313233
T0.0361 Å20.0088 Å2-0.0052 Å2--0.1099 Å2-0.0067 Å2---0.1031 Å2
L1.2211 °21.2961 °2-0.1862 °2-3.7628 °2-0.9833 °2--0.9953 °2
S0.0494 Å °-0.0488 Å °-0.0237 Å °-0.0488 Å °-0.0962 Å °0.025 Å °-0.0237 Å °0.025 Å °0.0468 Å °
Refinement TLS groupSelection details: { A|* }

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