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- PDB-3hfc: A trimeric form of the Kv7.1 A domain Tail, L602M/L606M mutant Semet -

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Basic information

Entry
Database: PDB / ID: 3hfc
TitleA trimeric form of the Kv7.1 A domain Tail, L602M/L606M mutant Semet
ComponentsPotassium voltage-gated channel subfamily KQT member 1
KeywordsTRANSPORT PROTEIN / coiled coil / trimer / Alternative splicing / Atrial fibrillation / Cell membrane / Cytoplasmic vesicle / Deafness / Disease mutation / Glycoprotein / Ion transport / Ionic channel / Long QT syndrome / Membrane / Phosphoprotein / Polymorphism / Potassium / Potassium channel / Potassium transport / Short QT syndrome / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information


gastrin-induced gastric acid secretion / stomach development / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / basolateral part of cell / lumenal side of membrane / negative regulation of delayed rectifier potassium channel activity / rhythmic behavior / regulation of gastric acid secretion ...gastrin-induced gastric acid secretion / stomach development / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / basolateral part of cell / lumenal side of membrane / negative regulation of delayed rectifier potassium channel activity / rhythmic behavior / 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 action potential / auditory receptor cell development / membrane repolarization during atrial cardiac muscle cell action potential / iodide transport / Phase 2 - plateau phase / intracellular chloride ion homeostasis / regulation of atrial cardiac muscle cell membrane repolarization / membrane repolarization during ventricular cardiac muscle cell action potential / atrial cardiac muscle cell action potential / renal sodium ion absorption / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / detection of mechanical stimulus involved in sensory perception of sound / membrane repolarization during cardiac muscle cell action potential / protein phosphatase 1 binding / intestinal absorption / potassium ion homeostasis / delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / non-motile cilium assembly / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of potassium ion transmembrane transport / inner ear morphogenesis / Voltage gated Potassium channels / outward rectifier potassium channel activity / regulation of heart contraction / cardiac muscle cell contraction / adrenergic receptor signaling pathway / inner ear development / monoatomic ion channel complex / renal absorption / protein kinase A regulatory subunit binding / ciliary base / protein kinase A catalytic subunit binding / potassium ion import across plasma membrane / social behavior / regulation of heart rate by cardiac conduction / cochlea development / action potential / voltage-gated potassium channel activity / positive regulation of heart rate / cardiac muscle contraction / transport vesicle / sensory perception of sound / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of cardiac muscle contraction / voltage-gated potassium channel complex / cellular response to epinephrine stimulus / cellular response to cAMP / potassium ion transmembrane transport / cytoplasmic vesicle membrane / erythrocyte differentiation / cellular response to xenobiotic stimulus / glucose metabolic process / response to insulin / regulation of membrane potential / regulation of blood pressure / heart development / late endosome / scaffold protein binding / basolateral plasma membrane / early endosome / transmembrane transporter binding / calmodulin binding / lysosome / apical plasma membrane / neuron projection / membrane raft / ubiquitin protein ligase binding / neuronal cell body / endoplasmic reticulum / membrane / plasma membrane / cytoplasm
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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily KQT member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsXu, Q. / Minor, D.L.
CitationJournal: Protein Sci. / Year: 2009
Title: Crystal structure of a trimeric form of the K(V)7.1 (KCNQ1) A-domain tail coiled-coil reveals structural plasticity and context dependent changes in a putative coiled-coil trimerization motif.
Authors: Xu, Q. / Minor, D.L.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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: Potassium voltage-gated channel subfamily KQT member 1


Theoretical massNumber of molelcules
Total (without water)10,5983
Polymers10,5983
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-26 kcal/mol
Surface area5050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.431, 41.232, 34.723
Angle α, β, γ (deg.)90.000, 119.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3532.663 Da / Num. of mol.: 3 / Fragment: UNP residues 583-611 / Mutation: L602M
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) / Strain (production host): BL21(pLys)S / References: UniProt: P51787
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.78 Å3/Da / Density % sol: 30.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. all: 2822 / Num. obs: 2774 / % possible obs: 98.3 % / Redundancy: 6.6 % / Rsym value: 0.101
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 238 / Rsym value: 0.203 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→32.48 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.862 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.153 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.344
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 120 4.6 %RANDOM
Rwork0.221 ---
obs0.223 2600 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.33 Å2 / Biso mean: 30.472 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å20 Å22.16 Å2
2---0.8 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.45→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms609 0 0 12 621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022608
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.973814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.058574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2124.19431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.08715128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.99159
X-RAY DIFFRACTIONr_chiral_restr0.120.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02441
X-RAY DIFFRACTIONr_nbd_refined0.2750.2298
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2433
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.23
X-RAY DIFFRACTIONr_mcbond_it1.6831.5396
X-RAY DIFFRACTIONr_mcangle_it1.792619
X-RAY DIFFRACTIONr_scbond_it3.4923229
X-RAY DIFFRACTIONr_scangle_it5.2464.5195
LS refinement shellResolution: 2.45→2.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 7 -
Rwork0.23 116 -
all-123 -
obs--67.21 %

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