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- PDB-7vvh: Crystal Structure of the Kv7.1 C-terminal Domain in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7vvh
TitleCrystal Structure of the Kv7.1 C-terminal Domain in Complex with Calmodulin disease mutation E140G
Components
  • Calmodulin-1
  • Potassium voltage-gated channel subfamily KQT member 1,Potassium voltage-gated channel subfamily KQT member 1
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / KCNQ1 / CaM / SIGNALING PROTEIN / SIGNALING PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


gastrin-induced gastric acid secretion / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / basolateral part of cell / lumenal side of membrane / negative regulation of voltage-gated potassium channel activity / rhythmic behavior / iodide transport / regulation of gastric acid secretion / stomach development ...gastrin-induced gastric acid secretion / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / basolateral part of cell / lumenal side of membrane / negative regulation of voltage-gated potassium channel activity / rhythmic behavior / iodide transport / regulation of gastric acid secretion / stomach development / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during atrial cardiac muscle cell action potential / Phase 3 - rapid repolarisation / membrane repolarization during action potential / regulation of atrial cardiac muscle cell membrane repolarization / Phase 2 - plateau phase / intracellular chloride ion homeostasis / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / negative regulation of delayed rectifier potassium channel activity / renal sodium ion absorption / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / potassium ion export across plasma membrane / atrial cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / protein phosphatase 1 binding / delayed rectifier potassium channel activity / positive regulation of potassium ion transmembrane transport / ventricular cardiac muscle cell action potential / Voltage gated Potassium channels / potassium ion homeostasis / non-motile cilium assembly / regulation of ventricular cardiac muscle cell membrane repolarization / cardiac muscle cell contraction / outward rectifier potassium channel activity / CaM pathway / intestinal absorption / 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 / inner ear morphogenesis / 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 / adrenergic receptor signaling pathway / autophagosome membrane docking / cochlea development / presynaptic endocytosis / renal absorption / regulation of heart contraction / regulation of cardiac muscle cell action potential / ciliary base / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / protein kinase A regulatory subunit binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / protein kinase A catalytic subunit binding / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / social behavior / potassium ion import across plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / inner ear development / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / action potential / 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 / voltage-gated potassium channel activity / monoatomic ion channel complex / 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 / positive regulation of heart rate
Similarity search - Function
Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif ...Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.296 Å
AuthorsChen, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022073 China
CitationJournal: To Be Published
Title: Crystal Structure of the Kv7.1 C-terminal Domain in Complex with Calmodulin disease mutation F141L
Authors: Chen, L.
History
DepositionNov 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Potassium voltage-gated channel subfamily KQT member 1,Potassium voltage-gated channel subfamily KQT member 1
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9834
Polymers24,9032
Non-polymers802
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-62 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.775, 63.882, 79.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Potassium voltage-gated channel subfamily KQT member 1,Potassium voltage-gated channel subfamily KQT member 1 / IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1 / KQT-like 1 / Voltage- ...IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1 / KQT-like 1 / Voltage-gated potassium channel subunit Kv7.1


Mass: 8122.424 Da / Num. of mol.: 1 / Fragment: C-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ1, KCNA8, KCNA9, KVLQT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P51787
#2: Protein Calmodulin-1


Mass: 16780.482 Da / Num. of mol.: 1 / Fragment: E141G
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.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 25% PEG 1500, 0.1M MMT pH 9.0

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.296→50 Å / Num. obs: 9688 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Χ2: 0.771 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.345.30.7944780.8460.3740.8810.48299.4
2.34-2.385.50.6264740.890.2880.6910.51799.6
2.38-2.435.60.5644630.9610.2550.6210.53499.8
2.43-2.485.60.4754740.9550.2180.5240.514100
2.48-2.535.90.4544760.9390.2040.4990.58100
2.53-2.596.30.4094700.9710.1770.4470.589100
2.59-2.666.50.3494740.9850.1510.3810.596100
2.66-2.736.40.2964780.9750.1260.3220.61100
2.73-2.816.50.2554690.9810.1090.2780.604100
2.81-2.96.40.2144910.9810.0920.2340.646100
2.9-36.40.1574680.9860.0670.1710.732100
3-3.126.20.1394820.9830.0620.1520.846100
3.12-3.265.90.1154700.990.0510.1260.863100
3.26-3.446.20.0994980.9950.0430.1080.99100
3.44-3.656.60.0794850.9960.0340.0860.994100
3.65-3.936.50.074840.9970.030.0760.999100
3.93-4.336.20.0614850.9950.0270.0671.064100
4.33-4.955.70.0565110.9960.0250.0610.981100
4.95-6.246.20.0534990.9970.0230.0571.048100
6.24-505.40.0565590.9940.0270.0631.05299.3

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v0c

4v0c


Resolution: 2.296→36.273 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 967 10.02 %
Rwork0.2387 8683 -
obs0.2421 9650 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.17 Å2 / Biso mean: 66.6706 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.296→36.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 2 6 1576
Biso mean--73.91 51.38 -
Num. residues----209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2965-2.41750.41441270.346115094
2.4175-2.5690.3491370.30841217100
2.569-2.76730.33531370.30931225100
2.7673-3.04560.3311370.3031244100
3.0456-3.4860.32681380.27251233100
3.486-4.39080.28251400.21081271100
4.3908-36.2730.21571510.20591343100

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