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- PDB-4v0c: Crystal Structure of the Kv7.1 proximal C-terminal Domain in Comp... -

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Basic information

Entry
Database: PDB / ID: 4v0c
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 / VOLTAGE-DEPENDENT POTASSIUM CHANNELS / LONG QT SYNDROME / CALMODULIN
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 / stomach development / iodide transport / regulation of gastric acid secretion ...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 / stomach development / iodide transport / regulation of gastric acid secretion / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / Phase 3 - rapid repolarisation / membrane repolarization during atrial cardiac muscle cell action potential / membrane repolarization during action potential / Phase 2 - plateau phase / regulation of atrial cardiac muscle cell membrane repolarization / intracellular chloride ion homeostasis / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of delayed rectifier potassium channel activity / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / renal sodium ion absorption / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / atrial cardiac muscle cell action potential / : / : / : / : / auditory receptor cell development / regulation of membrane repolarization / protein phosphatase 1 binding / : / positive regulation of protein autophosphorylation / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of peptidyl-threonine phosphorylation / delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / potassium ion homeostasis / Voltage gated Potassium channels / positive regulation of potassium ion transmembrane transport / establishment of protein localization to mitochondrial membrane / regulation of ventricular cardiac muscle cell membrane repolarization / type 3 metabotropic glutamate receptor binding / non-motile cilium assembly / outward rectifier potassium channel activity / cardiac muscle cell contraction / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / intestinal absorption / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / 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 / response to corticosterone / 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 / adrenergic receptor signaling pathway / 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 / ciliary base / regulation of cardiac muscle cell action potential / regulation of heart contraction / presynaptic endocytosis / protein kinase A regulatory subunit binding / renal absorption / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / protein kinase A catalytic subunit binding / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / potassium ion import across plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / inner ear development / RHO GTPases activate PAKs / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / action potential / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / cochlea development / Calcineurin activates NFAT
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 domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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 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
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: 2.86 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
DepositionSep 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)60,9009
Polymers60,6824
Non-polymers2185
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-150.2 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.092, 152.092, 56.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein 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 / KV7.1 CHANNEL


Mass: 13488.251 Da / Num. of mol.: 2
Fragment: PROXIMAL C-TERMINAL DOMAIN, RESIDUES 352-396 AND RESIDUES 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(DE3) / References: UniProt: P51787
#2: Protein CALMODULIN / CAM / KV7.1 CHANNEL


Mass: 16852.545 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-149
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(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical ChemComp-SCN / THIOCYANATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.3 M POTASSIUM THIOCYANATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH=5.6, 5 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.924
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.924 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 17341 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 15.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.9
Reflection shellHighest resolution: 2.85 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 6.4 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
SHARPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.86→49.784 Å / SU ML: 0.32 / σ(F): 1.32 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 883 5.1 %
Rwork0.2259 --
obs0.228 17456 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→49.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 7 4 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063598
X-RAY DIFFRACTIONf_angle_d1.0494820
X-RAY DIFFRACTIONf_dihedral_angle_d16.311279
X-RAY DIFFRACTIONf_chiral_restr0.035531
X-RAY DIFFRACTIONf_plane_restr0.004646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8597-3.03880.28251400.28872721X-RAY DIFFRACTION99
3.0388-3.27340.34141510.29192716X-RAY DIFFRACTION100
3.2734-3.60280.30891580.26792759X-RAY DIFFRACTION100
3.6028-4.12390.28241550.22992736X-RAY DIFFRACTION100
4.1239-5.19480.20731390.20922779X-RAY DIFFRACTION100
5.1948-49.79130.26941400.20182862X-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)
10.6321-1.2405-0.10011.92330.0441-0.007-0.55150.70181.0119-0.0681-0.39840.33980.4095-0.07991.57330.8859-0.2852-0.08081.471-0.12131.4195-61.402753.653443.228
27.4699-0.7418-1.22858.28080.08166.9311-0.0019-0.06530.2388-0.3630.22541.53520.6671-0.4439-0.1670.4624-0.0833-0.06570.46530.1120.2742-59.461814.022713.9016
31.9717-0.6537-0.99023.681-0.21857.21530.42230.46230.0065-0.5095-0.0138-0.0182-0.39220.025-0.18920.67540.2225-0.09480.60840.0020.3906-48.7635-19.716-11.1132
45.71032.06090.81012.9802-3.24275.58910.95860.2865-0.4971-0.9792-0.92280.6065-0.145-1.03-0.08560.62130.1273-0.16970.627-0.00620.533-53.1692-34.0979-9.9393
53.3424-1.6926-1.07688.85376.91036.52070.0954-0.2844-0.04510.0631-0.10790.10380.0790.3930.04411.03490.03210.0020.43530.12640.3812-51.97210.57314.4453
67.3303-1.11921.35069.7371-2.52117.49360.22290.4372-0.2444-0.7157-0.0103-0.91240.18290.927-0.31180.8650.23960.0750.72840.02940.5037-40.4785-15.5955-16.1656
75.7105-5.89173.29796.228-2.58566.0564-0.43470.645-1.1254-0.23330.40342.23370.99441.2803-0.35351.34290.0946-0.0490.97550.13061.2772-58.4642-23.0969-21.1259
83.4648-2.39874.00628.21233.17649.7935-1.087-1.1644-2.273-2.78023.25054.29870.9823-5.63-1.03620.7493-0.2815-0.69211.28890.39781.5884-62.6759-37.9565-12.1793
99.89972.27950.30878.6401-2.67484.11980.152-0.3026-0.94771.0552-0.14511.5146-0.1799-0.4328-0.02060.66170.11070.2080.49640.11911.1044-57.455-32.18130.4011
103.8132-3.1896-2.33188.5752-2.87167.38560.51810.01610.64980.18931.53223.7299-0.129-4.1531-1.20340.73650.0441-0.00231.20860.07692.041-68.4007-29.73-5.215
119.65541.29570.43617.5858-0.56328.4195-0.6693-0.3198-0.8064-1.09290.5918-0.87010.84611.1357-0.12050.7141-0.0305-0.05910.5513-0.00220.4182-42.5955-2.694320.4466
121.3998-1.4082-0.08181.61120.11850.0233-0.8320.72621.505-0.99350.18010.5124-1.61480.98481.03612.01440.2453-0.3091-0.08220.07081.1885-43.396412.269211.4061
133.7639-3.01680.60616.57012.9463.0623-0.5334-1.65182.05981.16480.9453-0.5656-0.64560.9892-0.49931.2618-0.0484-0.24290.8054-0.19240.7611-43.19048.8326.9208
144.2243.41884.36173.15865.18541.9967-0.40360.13481.31770.64730.08111.2237-2.3867-2.6392-0.44291.7196-0.057-0.18970.6730.23130.3963-48.411-0.982127.9839
15-0.0015-0.1974-0.04218.59051.01560.1346-1.0296-0.2417-0.2147-0.2030.88691.78540.6266-0.052-1.70051.8211-0.6954-0.19420.95990.66660.917-62.49134.500526.7852
166.5945-3.49435.75761.9878-3.06475.2258-0.3536-0.9712-0.7970.17660.772-0.2872-1.80160.2656-0.3850.778-0.11010.06190.78040.09920.7272-68.424515.752919.9755
179.0807-1.42931.02216.4171-0.98133.7810.09751.07230.3511-0.6025-0.09610.77250.4016-0.5766-0.07650.7285-0.1172-0.22080.6079-0.030.8113-66.077713.85076.6351
182.1089-1.1314-0.90973.6722-0.3670.6272-0.41580.4634-0.5538-0.99880.16532.20240.2602-0.4369-0.1474-2.2972-1.83090.18021.6036-0.11681.5636-77.303810.29566.4145
197.1027-5.54890.25186.2969-4.14547.30810.99460.728-1.4302-2.8382-0.04331.72781.3603-0.7877-1.21141.1019-0.25880.00050.8730.12841.3828-71.05736.143816.5149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 330 THROUGH 354 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 355 THROUGH 395 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 396 THROUGH 535 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 354 THROUGH 390 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 391 THROUGH 535 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 5 THROUGH 72 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 73 THROUGH 81 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 82 THROUGH 98 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 99 THROUGH 125 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 126 THROUGH 147 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 3 THROUGH 38 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 39 THROUGH 47 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 48 THROUGH 64 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 65 THROUGH 73 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 74 THROUGH 81 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 82 THROUGH 92 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 93 THROUGH 126 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 127 THROUGH 137 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 138 THROUGH 147 )

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