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- PDB-9el6: Crystal Structure of the Kv7.1 C-terminal Domain in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 9el6
TitleCrystal Structure of the Kv7.1 C-terminal Domain in Complex with Calmodulin disease mutation F90L
Components
  • Calmodulin-1
  • KCNQ1 helixAB
KeywordsMETAL BINDING PROTEIN / calmodulin
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 / negative regulation of high voltage-gated calcium channel 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 / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / 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 / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / 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 / calcium channel inhibitor activity / cellular response to interferon-beta / Activation of AMPK downstream of NMDARs / Protein methylation / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / sperm midpiece / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Ras activation upon Ca2+ influx through NMDA receptor / 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 / positive regulation of receptor signaling pathway via JAK-STAT / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / 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 / Platelet degranulation / Inactivation, recovery and regulation of the phototransduction cascade / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLiu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of the Kv7.1 C-terminal Domain in Complex with Calmodulin disease mutation F90L
Authors: Liu, C.
History
DepositionDec 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KCNQ1 helixAB
C: Calmodulin-1
D: KCNQ1 helixAB
E: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,75210
Polymers49,5124
Non-polymers2406
Water1,15364
1
A: KCNQ1 helixAB
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8765
Polymers24,7562
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-77 kcal/mol
Surface area10350 Å2
MethodPISA
2
D: KCNQ1 helixAB
E: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8765
Polymers24,7562
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-76 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.249, 74.326, 130.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein KCNQ1 helixAB


Mass: 7937.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Calmodulin-1


Mass: 16818.529 Da / Num. of mol.: 2
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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M PCTP (pH8.0), 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.248→37.58 Å / Num. obs: 20150 / % possible obs: 98.97 % / Redundancy: 5.7 % / Biso Wilson estimate: 37.49 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.067 / Net I/σ(I): 6
Reflection shellResolution: 2.248→2.328 Å / Num. unique obs: 1915 / CC1/2: 0.725 / Rpim(I) all: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→37.58 Å / SU ML: 0.3074 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 38.309 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3015 1997 9.94 %
Rwork0.239 18090 -
obs0.2455 20087 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.22 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 6 64 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733100
X-RAY DIFFRACTIONf_angle_d0.85994199
X-RAY DIFFRACTIONf_chiral_restr0.0455483
X-RAY DIFFRACTIONf_plane_restr0.0051554
X-RAY DIFFRACTIONf_dihedral_angle_d5.01311859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.35251330.31481201X-RAY DIFFRACTION94.54
2.3-2.370.33461400.27941280X-RAY DIFFRACTION99.65
2.37-2.440.32091410.27541265X-RAY DIFFRACTION99.72
2.44-2.510.39521410.27731280X-RAY DIFFRACTION99.23
2.51-2.60.32451410.2721274X-RAY DIFFRACTION99.58
2.6-2.710.35751390.27781276X-RAY DIFFRACTION99.51
2.71-2.830.3631440.28271309X-RAY DIFFRACTION99.52
2.83-2.980.38961410.26251272X-RAY DIFFRACTION99.02
2.98-3.170.32471400.24791277X-RAY DIFFRACTION98.61
3.17-3.410.29861450.2411303X-RAY DIFFRACTION99.86
3.41-3.760.29171440.22491306X-RAY DIFFRACTION99.38
3.76-4.30.25121470.20731319X-RAY DIFFRACTION99.12
4.3-5.410.28561460.22071323X-RAY DIFFRACTION99.06
5.41-37.580.26391550.21481405X-RAY DIFFRACTION98.36

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