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- PDB-5j03: Crystal Structure of a chimeric Kv7.2 - Kv7.3 proximal C-terminal... -

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Basic information

Entry
Database: PDB / ID: 5j03
TitleCrystal Structure of a chimeric Kv7.2 - Kv7.3 proximal C-terminal Domain in Complex with Calmodulin
Components
  • Calmodulin
  • Potassium voltage-gated channel subfamily KQT member 3,Potassium voltage-gated channel subfamily KQT member 2
KeywordsTRANSPORT PROTEIN / voltage-gated potassium channel / complex / calmodulin
Function / homology
Function and homology information


axon initial segment / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / Voltage gated Potassium channels / node of Ranvier / membrane hyperpolarization / delayed rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / CaM pathway ...axon initial segment / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / Voltage gated Potassium channels / node of Ranvier / membrane hyperpolarization / delayed rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / CaM pathway / Interaction between L1 and Ankyrins / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ankyrin binding / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / plasma membrane => GO:0005886 / voltage-gated potassium channel activity / action potential / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of nitric-oxide synthase activity
Similarity search - Function
Potassium channel, voltage dependent, KCNQ3 / Voltage-gated potassium channel / Potassium channel, voltage dependent, KCNQ2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Unstructured region on Potassium channel subunit alpha KvLQT2 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / : ...Potassium channel, voltage dependent, KCNQ3 / Voltage-gated potassium channel / Potassium channel, voltage dependent, KCNQ2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Unstructured region on Potassium channel subunit alpha KvLQT2 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / : / 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
ACETATE ION / Potassium voltage-gated channel subfamily KQT member 3 / Potassium voltage-gated channel subfamily KQT member 2 / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStrulovich, R. / Hirsch, J.A.
Funding support Germany, Israel, 2items
OrganizationGrant numberCountry
German Research Foundation Germany
Israel Science Foundation1519/12 Israel
CitationJournal: Biochemistry / Year: 2016
Title: Structural Insights into the M-Channel Proximal C-Terminus/Calmodulin Complex.
Authors: Strulovich, R. / Tobelaim, W.S. / Attali, B. / Hirsch, J.A.
History
DepositionMar 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 2.0Oct 16, 2019Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / pdbx_audit_support / reflns_shell
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_symmetry / _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_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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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 3,Potassium voltage-gated channel subfamily KQT member 2
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1798
Polymers29,9192
Non-polymers2596
Water2,396133
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-96 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.665, 47.665, 182.216
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-387-

HOH

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Components

#1: Protein Potassium voltage-gated channel subfamily KQT member 3,Potassium voltage-gated channel subfamily KQT member 2 / KQT-like 3 / Potassium channel subunit alpha KvLQT3 / Voltage-gated potassium channel subunit Kv7.3 ...KQT-like 3 / Potassium channel subunit alpha KvLQT3 / Voltage-gated potassium channel subunit Kv7.3 / KQT-like 2 / Neuroblastoma-specific potassium channel subunit alpha KvLQT2 / Voltage-gated potassium channel subunit Kv7.2


Mass: 13066.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence is chimeric. Residues 29-82 correspond to human Kv7.3 (KCNQ3), residues 356-409 (Uniprot O43525-1). Residues 83-110 correspond to human Kv7.2 (KCNQ2), residues 530-557 (Uniprot O43526-1).
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ3, KCNQ2 / Production host: Escherichia coli (E. coli) / References: UniProt: O43525, UniProt: O43526
#2: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is mammalian calmodulin with four bound Ca2+ ions. The initiating methionine residue is cleaved in vivo.
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 18% PEG 4K and 100 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→40.259 Å / Num. obs: 17064 / % possible obs: 99.92 % / Redundancy: 5.9 % / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.259 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 919 5.39 %
Rwork0.1786 --
obs0.1814 17064 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 9 133 1855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131759
X-RAY DIFFRACTIONf_angle_d1.2162372
X-RAY DIFFRACTIONf_dihedral_angle_d11.6231072
X-RAY DIFFRACTIONf_chiral_restr0.058261
X-RAY DIFFRACTIONf_plane_restr0.007317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10550.28971070.24692244X-RAY DIFFRACTION100
2.1055-2.23740.22571680.2052224X-RAY DIFFRACTION100
2.2374-2.41010.21091190.18192280X-RAY DIFFRACTION100
2.4101-2.65260.23311160.18172301X-RAY DIFFRACTION100
2.6526-3.03630.24241260.19152301X-RAY DIFFRACTION100
3.0363-3.8250.23561380.17112315X-RAY DIFFRACTION100
3.825-40.26710.21251450.16112480X-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)
14.9269-4.3335-2.08574.06592.77854.2847-1.2939-1.1485-1.0712-0.80171.5496-0.31210.57420.91460.16470.75910.0880.20820.78220.25081.295431.5362-14.89976.5603
26.6759-6.1987-1.91085.86832.15292.2365-0.3828-0.5303-0.67641.16940.28640.22031.0023-0.32490.12590.4964-0.05180.01960.25330.02390.342428.3918-7.204912.2512
33.3894-2.5243-0.43693.6781-1.49663.0205-0.3094-0.1620.05940.24150.28180.0097-0.0909-0.05150.03450.332-0.0866-0.00470.2295-0.04610.224126.38647.994511.7049
45.4853-2.02922.02380.7554-0.86372.1407-0.1594-0.06831.02391.2780.0221-0.6037-0.28980.6453-0.04590.5577-0.0868-0.10160.2981-0.12070.499625.820822.42099.8415
56.06090.718-5.42662.3915-2.1438.2065-0.36770.4584-0.54090.47980.2834-0.2371-0.2433-0.32670.14450.3837-0.00390.0790.2164-0.04380.244519.26217.19429.2575
62.68530.967-0.11176.58075.34134.69550.6339-0.85180.08271.8314-1.52420.8645-0.5863-0.19870.96120.7075-0.24630.15140.4636-0.0510.511912.74712.646114.0234
73.30442.477-2.22718.02993.15095.32190.4485-0.66660.71441.0161-0.61270.997-0.4715-2.12450.2970.86160.1485-0.05391.00520.01730.471312.858620.540820.2919
88.5329-3.6218-0.0871.8878-1.40676.2422-0.03560.14030.3892-0.0803-0.12450.0946-1.8908-0.0150.37010.6170.0165-0.02490.2333-0.01950.245523.39415.019920.7915
93.541-2.5323-1.70183.2007-1.45036.0493-0.16980.2978-0.0592-0.3130.2040.02740.20060.0026-0.01730.3275-0.0558-0.00180.25-0.03390.237929.95315.220719.1322
109.899-1.38222.70274.90283.95274.7465-0.4408-0.9926-0.94991.64760.2670.09850.17210.88410.04590.48290.03320.06480.48990.09050.469834.4968-2.05219.5347
113.09693.249-1.95953.426-2.05541.22780.71133.75982.5951-0.1839-1.0135-1.0251-0.97040.87640.14780.4363-0.03830.00310.85820.32890.689932.817329.234921.9248
127.18324.2389-5.27432.5989-3.63927.45130.22070.30050.14430.60650.4240.6133-1.3186-0.9991-0.70470.46590.1119-0.05040.48570.11780.280627.037925.735726.628
136.97911.68132.36362.5826-2.40144.9255-0.0141-0.211-0.36170.6962-0.19470.9665-0.51180.28850.050.38790.08910.08430.35660.01130.308821.683819.23131.3254
148.3852-0.3696-6.38139.60593.09945.6859-0.0503-0.5142-0.11781.759-0.02741.01280.2859-0.06510.07380.57830.06830.16280.4380.06910.371321.953215.359138.1407
151.57382.16992.27157.18713.73075.2469-0.0879-0.8326-0.52150.69120.11741.5585-0.2634-0.09130.02690.37220.05210.2090.39050.16310.611518.89089.005433.2596
169.15543.41643.34266.48580.19465.5-0.3970.2972-0.8032-0.39470.99291.07980.357-1.1582-0.26860.3076-0.1185-0.01910.50170.12420.822914.66649.722425.8195
173.1612-1.8914-0.41413.5877-2.58366.9907-1.4202-0.6071-0.2321-0.21040.42641.5103-0.1197-0.31711.16970.645-0.03260.01620.39630.08980.906317.57142.035427.192
185.83375.0908-6.85494.6149-5.53039.7674-0.784-0.1543-1.1823-0.5322-0.20670.08410.88460.00820.83530.4966-0.01120.05940.260.0460.42424.96572.252828.4358
197.88642.69943.58074.51734.94735.40930.2055-0.5206-0.4946-0.13220.1626-0.06250.68350.1556-0.42440.45170.1341-0.07690.37390.03610.288832.98678.140931.1011
202.67031.0825-1.65597.0109-0.04911.66970.0285-0.6496-0.09820.44660.0581-0.10670.22720.2567-0.19320.36030.0234-0.05170.31460.02820.193631.51515.270632.5588
215.1845-3.6796-3.58877.92616.1774.9711-0.45470.9436-1.0229-0.62811.0813-0.65750.8096-0.5747-0.40590.6969-0.1720.02160.2966-0.14620.323933.689215.898220.4373
223.4722-0.74810.52252.23191.99712.19920.21980.2750.6146-0.3466-0.3152-1.7566-0.79820.4333-0.28510.5233-0.1275-0.05270.3969-0.00630.533738.90159.154613.3251
236.06526.16376.04966.25016.16936.0721-0.25640.4536-0.5333-0.30450.2906-1.11160.02471.3443-0.10960.3012-0.05040.04450.28450.0060.362534.2807-0.48496.0957
247.2648-1.52213.08666.02651.73245.3042-0.2410.8133-0.30420.1633-0.0121-0.56470.11640.18360.24120.4089-0.09380.15110.3005-0.09670.356333.0597-2.7768-3.345
258.39450.0556-5.48533.982-2.26647.6299-0.06290.1828-0.1781-0.22680.0907-0.0103-0.08530.1165-0.20690.3341-0.1086-0.00510.2482-0.06360.312622.63911.0337-1.5136
263.97660.0118-0.41525.5697-2.26683.28350.06570.0458-0.33510.2759-0.03790.36030.3967-0.27480.04420.3447-0.09580.0380.2252-0.0420.288118.72720.58867.5437
279.10.7855-6.16316.8939-1.85327.26040.17880.1036-0.1376-0.3402-0.14080.3311-0.0648-0.57190.22310.3254-0.0331-0.00680.2508-0.06610.244619.45559.95363.8438
284.11180.124-0.63337.3863.83529.6775-0.16130.29790.2102-0.52980.257-0.0169-0.374-0.1388-0.06580.3787-0.09460.03890.287-0.02290.223926.954910.2193-4.8879
292.36034.11953.10219.61232.11368.5162-0.02290.22830.2836-0.40380.0857-0.7937-0.06530.44410.06440.3407-0.08510.0950.2398-0.02010.321534.53616.4693-0.3587
308.86642.65422.90844.6374.62444.65150.9940.00270.79120.5067-0.54180.799-0.89760.184-0.39350.3811-0.09540.05920.31780.02530.325136.234312.21475.8608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 350:358)
2X-RAY DIFFRACTION2(chain A and resid 359:363)
3X-RAY DIFFRACTION3(chain A and resid 364:377)
4X-RAY DIFFRACTION4(chain A and resid 378:382)
5X-RAY DIFFRACTION5(chain A and resid 383:388)
6X-RAY DIFFRACTION6(chain A and resid 389:394)
7X-RAY DIFFRACTION7(chain A and resid 395:536)
8X-RAY DIFFRACTION8(chain A and resid 537:546)
9X-RAY DIFFRACTION9(chain A and resid 547:552)
10X-RAY DIFFRACTION10(chain A and resid 553:557)
11X-RAY DIFFRACTION11(chain B and resid 3:9)
12X-RAY DIFFRACTION12(chain B and resid 10:14)
13X-RAY DIFFRACTION13(chain B and resid 15:21)
14X-RAY DIFFRACTION14(chain B and resid 22:29)
15X-RAY DIFFRACTION15(chain B and resid 30:35)
16X-RAY DIFFRACTION16(chain B and resid 36:41)
17X-RAY DIFFRACTION17(chain B and resid 42:46)
18X-RAY DIFFRACTION18(chain B and resid 47:52)
19X-RAY DIFFRACTION19(chain B and resid 53:59)
20X-RAY DIFFRACTION20(chain B and resid 60:71)
21X-RAY DIFFRACTION21(chain B and resid 72:77)
22X-RAY DIFFRACTION22(chain B and resid 78:85)
23X-RAY DIFFRACTION23(chain B and resid 86:93)
24X-RAY DIFFRACTION24(chain B and resid 94:101)
25X-RAY DIFFRACTION25(chain B and resid 102:107)
26X-RAY DIFFRACTION26(chain B and resid 108:119)
27X-RAY DIFFRACTION27(chain B and resid 120:125)
28X-RAY DIFFRACTION28(chain B and resid 126:136)
29X-RAY DIFFRACTION29(chain B and resid 137:142)
30X-RAY DIFFRACTION30(chain B and resid 143:148)

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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