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

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Basic information

Entry
Database: PDB / ID: 7vvd
TitleCrystal Structure of the Kv7.1 C-terminal Domain in Complex with Calmodulin disease mutation Q135P
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 / Calcineurin activates NFAT / protein phosphatase activator activity / Regulation of MECP2 expression and activity / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated potassium channel activity / DARPP-32 events / 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: 3.134 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 5, 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

Downloads & links

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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
D: Potassium voltage-gated channel subfamily KQT member 1,Potassium voltage-gated channel subfamily KQT member 1
E: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0488
Polymers49,8884
Non-polymers1604
Water362
1
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)25,0244
Polymers24,9442
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-46 kcal/mol
Surface area10790 Å2
MethodPISA
2
D: Potassium voltage-gated channel subfamily KQT member 1,Potassium voltage-gated channel subfamily KQT member 1
E: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0244
Polymers24,9442
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-46 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.505, 86.270, 126.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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: 16821.531 Da / Num. of mol.: 2 / Mutation: Q135P
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.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% PEG 1500, 0.1M MMT pH 8.0

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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: 3.134→50 Å / Num. obs: 7537 / % possible obs: 93.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.058 / Rrim(I) all: 0.131 / Χ2: 0.804 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.24.40.6213550.5720.3420.7130.46696.7
3.2-3.264.40.6343850.4920.3340.720.49692.3
3.26-3.334.50.4953650.6970.2560.560.49396.8
3.33-3.394.80.4343650.870.2180.4870.50290.3
3.39-3.475.10.3983600.8630.1950.4450.51994.2
3.47-3.554.90.3013680.9350.150.3380.57993.4
3.55-3.644.90.2493670.9610.1250.280.6892.9
3.64-3.734.90.223690.9470.1090.2470.71592.2
3.73-3.8450.1893670.9450.0930.2120.69594.1
3.84-3.974.80.1533710.9590.0770.1720.84893.2
3.97-4.114.90.1363710.9790.0670.1520.9591.4
4.11-4.274.90.1253570.9650.0640.1411.00191.1
4.27-4.474.70.1153840.9640.060.131.03592.8
4.47-4.74.50.1113550.9850.0580.1261.07989.9
4.7-54.90.1013720.9910.050.1130.99391.2
5-5.385.60.1013580.9910.0450.1110.90589.7
5.38-5.935.50.13820.9920.0460.110.89491
5.93-6.785.50.0853990.9930.0390.0940.995
6.78-8.545.10.0614250.9970.0290.0681.01499.8
8.54-505.20.0494620.9970.0230.0541.05998.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V0C

4v0c


Resolution: 3.134→37.793 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 752 10.01 %RANDOM
Rwork0.2434 6762 --
obs0.2464 7514 91.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.34 Å2 / Biso mean: 57.1726 Å2 / Biso min: 39.48 Å2
Refinement stepCycle: final / Resolution: 3.134→37.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 4 2 2966
Biso mean--55.63 56.51 -
Num. residues----409
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.134-3.37540.33091330.3053119782
3.3754-3.71490.29181500.2659134493
3.7149-4.25180.25081500.2233135493
4.2518-5.35440.25661500.2324134990
5.3544-37.7930.27811690.2376151896

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