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- PDB-4umo: Crystal Structure of the Kv7.1 proximal C-terminal Domain in Comp... -

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Basic information

Entry
Database: PDB / ID: 4umo
TitleCrystal Structure of the Kv7.1 proximal C-terminal Domain in Complex with Calmodulin
Components
  • CALMODULIN
  • POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY KQT MEMBER 1
KeywordsSIGNALING PROTEIN / LONG QT SYNDROME
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 / regulation of gastric acid secretion / stomach development / membrane repolarization during atrial cardiac muscle cell action potential ...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 / regulation of gastric acid secretion / stomach development / membrane repolarization during atrial cardiac muscle cell action potential / Phase 3 - rapid repolarisation / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / membrane repolarization during ventricular cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane repolarization / iodide transport / Phase 2 - plateau phase / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / intracellular chloride ion homeostasis / renal sodium ion absorption / negative regulation of delayed rectifier potassium channel activity / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / atrial cardiac muscle cell action potential / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / regulation of membrane repolarization / protein phosphatase 1 binding / delayed rectifier potassium channel activity / : / positive regulation of potassium ion transmembrane transport / establishment of protein localization to mitochondrial membrane / Voltage gated Potassium channels / type 3 metabotropic glutamate receptor binding / outward rectifier potassium channel activity / potassium ion homeostasis / ventricular cardiac muscle cell action potential / non-motile cilium assembly / regulation of ventricular cardiac muscle cell membrane repolarization / CaM pathway / Cam-PDE 1 activation / intestinal absorption / Sodium/Calcium exchangers / regulation of heart contraction / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / ciliary base / monoatomic ion channel complex / regulation of synaptic vesicle exocytosis / inner ear morphogenesis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / positive regulation of heart rate / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / response to corticosterone / cochlea development / renal absorption / adrenergic receptor signaling pathway / positive regulation of ryanodine-sensitive calcium-release channel activity / potassium ion import across plasma membrane / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / protein kinase A regulatory subunit binding / protein phosphatase activator activity / RHO GTPases activate PAKs / voltage-gated potassium channel activity / protein kinase A catalytic subunit binding / inner ear development / social behavior / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity
Similarity search - Function
Helix Hairpins - #1910 / Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Helix Hairpins / Voltage-dependent channel domain superfamily / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif ...Helix Hairpins - #1910 / Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Helix Hairpins / Voltage-dependent channel domain superfamily / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / THIOCYANATE ION / Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1 / Calmodulin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSachyani, D. / Hirsch, J.A.
CitationJournal: Structure / Year: 2014
Title: Structural Basis of a Kv7.1 Potassium Channel Gating Module: Studies of the Intracellular C-Terminal Domain in Complex with Calmodulin
Authors: Sachyani, D. / Dvir, M. / Strulovich, R. / Tria, G. / Tobelaim, W. / Peretz, A. / Pongs, O. / Svergun, D. / Attali, B. / Hirsch, J.A.
History
DepositionMay 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

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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
B: POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY KQT MEMBER 1
C: CALMODULIN
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,95613
Polymers60,5814
Non-polymers3759
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-137.8 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.760, 151.760, 56.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY KQT MEMBER 1 / KV7.1 CHANNEL / IKS PRODUCING SLOW VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT ALPHA KVLQT1 / KQT-LIKE ...KV7.1 CHANNEL / IKS PRODUCING SLOW VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT ALPHA KVLQT1 / KQT-LIKE 1 / VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT KV7.1


Mass: 13438.191 Da / Num. of mol.: 2
Fragment: PROXIMAL C-TERMINAL DOMAIN, RESIDUES 352-396,502-539
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P51787
#2: Protein CALMODULIN / / CAM


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS

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Non-polymers , 4 types, 10 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 % / Description: NONE
Crystal growTemperature: 277 K
Details: 0.3 M POTASSIUM THIOCYANATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH=5.6, 1 MM EGTA AT 4 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.974
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15107 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 40.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3→49.675 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 757 5 %
Rwork0.2133 --
obs0.215 15006 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 11 1 3518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053594
X-RAY DIFFRACTIONf_angle_d0.8944813
X-RAY DIFFRACTIONf_dihedral_angle_d14.9421282
X-RAY DIFFRACTIONf_chiral_restr0.036528
X-RAY DIFFRACTIONf_plane_restr0.004645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.23180.32351590.2822795X-RAY DIFFRACTION100
3.2318-3.5570.2651460.24222836X-RAY DIFFRACTION100
3.557-4.07150.23711510.21332821X-RAY DIFFRACTION100
4.0715-5.12880.23021470.19092868X-RAY DIFFRACTION100
5.1288-49.68190.23771540.20452929X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.11550.32980.80610.00210.08945.95380.25110.30050.08460.37920.003-0.0101-0.46020.1619-0.16670.71640.0699-0.12610.2983-0.13740.479852.3230.873831.0243
27.5081-5.14196.19089.3658-5.66138.5934-0.3487-0.59970.362-0.55390.6935-0.26450.1514-0.4046-0.20430.45680.20660.08830.7772-0.05420.298422.922746.75156.9513
34.4254-2.55474.61081.908-1.77673.7659-0.20940.43920.33240.0996-0.05240.405-0.3550.4070.38950.3327-0.0503-0.00040.56640.11480.73473.973867.4757-2.749
47.1954-5.35.42695.8756-5.77448.84180.48460.0147-0.18410.4646-0.0977-0.0420.1742-0.16930.04150.57370.2698-0.04990.4975-0.1320.24638.588735.752731.0347
58.6485-3.2674-4.61946.96691.68172.4433-0.3304-1.30790.2112-0.77270.4633-0.8261.11121.4671-0.18350.79740.0842-0.00430.8766-0.16260.429231.340537.00210.2373
65.8603-3.0065-4.93473.13411.23695.2128-0.21320.2205-0.23370.1416-1.50221.27532.5553-1.25641.60911.185-0.277-0.25520.89390.05980.805818.004930.55131.1249
73.3181-1.74282.25985.7880.53267.1768-0.018-1.63020.09321.3374-0.05481.41090.786-1.53040.03850.4626-0.03010.15670.78730.06350.548813.929439.0711.0781
86.5609-2.1021-5.18396.66311.73375.51230.62470.46381.1269-0.7543-0.01480.4623-0.1244-1.2079-0.39030.35510.0746-0.16640.8118-0.12810.437711.524644.3941.5408
96.25530.04816.55352.0402-1.11018.6550.28522.8385-0.9505-3.12260.46591.22271.8182-1.5543-0.76120.97490.0116-0.30971.12950.07150.764714.948638.4179-6.9899
106.2741.1167-2.67514.7223.1876.56250.01690.91080.5505-1.67220.46510.4928-1.1335-0.6412-0.43850.64610.30760.12920.8829-0.06110.364825.672144.9976-3.7199
113.2198-3.003-3.42814.42214.91196.31250.9383-0.38710.5519-0.8588-0.4788-0.1571-1.13920.9457-0.40140.7676-0.1230.16530.7603-0.00710.76223.213464.97560.5173
123.44390.26782.18883.6816-2.13523.03680.24490.33231.0379-0.5737-0.5236-1.122-3.19172.7333-0.10191.4536-0.41710.54311.15740.09351.246618.524473.77978.6581
135.11430.9914-4.18260.6202-1.99236.64690.4454-1.19231.50040.7341-0.12931.2324-1.76371.7802-0.2690.5618-0.0923-0.00880.5288-0.15730.931919.297466.633217.0742
148.2673-4.04983.39365.2309-5.35418.5167-1.3105-1.15470.98560.3360.6105-0.51381.1598-1.3466-0.74230.4612-0.0348-0.08140.8781-0.10130.584716.004955.980316.0268
152.00099.5989-5.32439.8382-3.95224.59571.3365-2.9038-0.95433.0145-2.0508-2.06610.04171.37990.37920.6582-0.0501-0.27261.1981-0.28890.909727.104359.613520.005
160.18320.9375-1.30514.7835-6.65179.2483-0.4771-0.48060.52961.2646-0.6109-2.1916-1.22572.65950.49420.777-0.0919-0.17731.4757-0.41121.918430.958572.796318.3598
172.7834-4.02631.77498.1738-0.02343.88460.90260.63142.8659-0.21250.1277-1.7512-1.73341.3122-0.86040.1012-0.20280.30310.8259-0.17141.466329.581266.19157.9427
188.9082-1.6733-2.64927.51613.11532.3188-0.1761-0.50030.7905-0.11220.4244-0.3432-0.6170.1577-0.08080.92460.30260.09111.0048-0.04410.480729.127737.586140.0013
197.0836-2.7492-0.97925.81740.62468.4576-0.3056-0.6402-0.72140.6180.5855-0.27560.882-0.2363-0.32210.82210.18570.02630.39210.03810.398736.125.601239.7335
204.204-5.21980.65616.85760.34143.03730.4447-1.6566-0.21970.10230.5498-1.271-1.2131.846-1.28191.1118-0.2076-0.36980.9213-0.36821.482661.936435.702537.2504
214.26585.0435-1.52196.98410.73247.23850.03311.17281.0695-1.06910.0081-1.3961-0.41980.0217-0.2630.49060.07210.15170.37570.09211.009455.98134.710922.9225
223.39550.9320.25851.48810.13021.1848-0.62480.3921.247-0.93430.7384-0.7606-0.93180.50250.3490.4582-0.60220.03150.1161-0.46121.942460.371943.757729.9485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 356 THROUGH 395 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 396 THROUGH 535 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 328 THROUGH 385 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 386 THROUGH 535 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 3 THROUGH 19 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 20 THROUGH 28 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 29 THROUGH 44 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 45 THROUGH 55 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 56 THROUGH 64 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 65 THROUGH 77 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 78 THROUGH 90 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 91 THROUGH 98 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 99 THROUGH 111 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 112 THROUGH 117 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 118 THROUGH 128 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 129 THROUGH 134 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 135 THROUGH 147 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 5 THROUGH 19 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 20 THROUGH 78 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 79 THROUGH 98 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 99 THROUGH 128 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 129 THROUGH 147 )

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