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- PDB-9jqi: Crystal structure of calmodulin in complex with KN93 (1:1 complex) -

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Basic information

Entry
Database: PDB / ID: 9jqi
TitleCrystal structure of calmodulin in complex with KN93 (1:1 complex)
ComponentsCalmodulin-1
KeywordsMETAL BINDING PROTEIN / calmodulin / KN93
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 / CaMK IV-mediated phosphorylation of CREB ...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 / 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 / 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 / regulation of cell communication by electrical coupling involved in cardiac conduction / 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 / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / 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 / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / 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 / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / cellular response to type II interferon / Stimuli-sensing channels / G2/M transition of mitotic cell cycle / long-term synaptic potentiation / spindle pole / RAS processing / Signaling by RAF1 mutants / calcium-dependent protein binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / myelin sheath / RAF/MAP kinase cascade / Ca2+ pathway / 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 / calcium ion binding
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-KN9 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Crystal structure of calmodulin in complex with KN93 (1:1 complex)
Authors: Liu, X.C.
History
DepositionSep 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
B: Calmodulin-1
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,67818
Polymers53,6943
Non-polymers1,98415
Water1,63991
1
A: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5596
Polymers17,8981
Non-polymers6615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area8620 Å2
MethodPISA
2
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5596
Polymers17,8981
Non-polymers6615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area8530 Å2
MethodPISA
3
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5596
Polymers17,8981
Non-polymers6615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.336, 40.264, 173.413
Angle α, β, γ (deg.)90.000, 92.470, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Calmodulin-1


Mass: 17898.125 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DP23
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-KN9 / N-[2-[[[3-(4'-Chlorophenyl)-2-propenyl]methylamino]methyl]phenyl]-N-(2-hydroxyethyl)-4'-methoxybenzenesulfonamide / N-[2-({[(2E)-3-(4-chlorophenyl)prop-2-en-1-yl](methyl)amino}methyl)phenyl]-N-(2-hydroxyethyl)-4-methoxybenzene-1-sulfonamide


Mass: 501.037 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H29ClN2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: sodium acetate, sodium cacodylate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.1→57.75 Å / Num. obs: 28412 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.158 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4103 / CC1/2: 0.775 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPXdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6m7h

6m7h


Resolution: 2.1→57.75 Å / SU ML: 0.3195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2882 1999 7.04 %
Rwork0.2484 26411 -
obs0.2512 28410 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→57.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 114 91 3499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023445
X-RAY DIFFRACTIONf_angle_d0.50424628
X-RAY DIFFRACTIONf_chiral_restr0.0348493
X-RAY DIFFRACTIONf_plane_restr0.0034626
X-RAY DIFFRACTIONf_dihedral_angle_d12.5034468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.34341380.29781824X-RAY DIFFRACTION99.95
2.15-2.210.33961490.26851889X-RAY DIFFRACTION99.95
2.21-2.270.32181370.28111836X-RAY DIFFRACTION99.6
2.27-2.350.32781340.26751934X-RAY DIFFRACTION100
2.35-2.430.34371400.26321818X-RAY DIFFRACTION100
2.43-2.530.30951490.26281921X-RAY DIFFRACTION100
2.53-2.640.33961400.25681863X-RAY DIFFRACTION99.95
2.64-2.780.2931450.25391869X-RAY DIFFRACTION99.75
2.78-2.960.34131350.27691876X-RAY DIFFRACTION99.95
2.96-3.190.30971270.26371895X-RAY DIFFRACTION100
3.19-3.510.29221570.24961883X-RAY DIFFRACTION100
3.51-4.010.24611550.23071928X-RAY DIFFRACTION99.76
4.01-5.060.24921400.21381917X-RAY DIFFRACTION99.9
5.06-57.750.26321530.24091958X-RAY DIFFRACTION99.39

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