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- PDB-3hfe: A trimeric form of the Kv7.1 A domain Tail -

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Basic information

Entry
Database: PDB / ID: 3hfe
TitleA trimeric form of the Kv7.1 A domain Tail
ComponentsPotassium voltage-gated channel subfamily KQT member 1
KeywordsTRANSPORT PROTEIN / trimer / Atrial fibrillation / Cell membrane / Cytoplasmic vesicle / Deafness / Disease mutation / Glycoprotein / Ion transport / Ionic channel / Long QT syndrome / Membrane / Phosphoprotein / Potassium / Potassium channel / Potassium transport / Short QT syndrome / Transmembrane / Transport / Voltage-gated channel
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 / delayed rectifier potassium channel activity / protein phosphatase 1 binding / positive regulation of potassium ion transmembrane transport / Voltage gated Potassium channels / 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 / intestinal absorption / regulation of heart contraction / monoatomic ion channel complex / ciliary base / inner ear morphogenesis / positive regulation of heart rate / cochlea development / renal absorption / adrenergic receptor signaling pathway / potassium ion import across plasma membrane / protein kinase A regulatory subunit binding / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / protein kinase A catalytic subunit binding / inner ear development / social behavior / voltage-gated potassium channel complex / cellular response to cAMP / transport vesicle / positive regulation of cardiac muscle contraction / potassium ion transmembrane transport / cardiac muscle contraction / cellular response to epinephrine stimulus / phosphatidylinositol-4,5-bisphosphate binding / erythrocyte differentiation / sensory perception of sound / response to insulin / cytoplasmic vesicle membrane / regulation of blood pressure / glucose metabolic process / cellular response to xenobiotic stimulus / late endosome / heart development / scaffold protein binding / basolateral plasma membrane / transmembrane transporter binding / lysosome / calmodulin binding / early endosome / neuron projection / membrane raft / apical plasma membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)10,1603
Polymers10,1603
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-20 kcal/mol
Surface area5170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.789, 40.838, 34.830
Angle α, β, γ (deg.)90.000, 118.410, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-59-

HOH

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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: 3386.797 Da / Num. of mol.: 3 / Fragment: UNP residues 583-611
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 / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.84 Å3/Da / Density % sol: 33.17 %
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

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 8174 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.102 / Χ2: 1.6 / Net I/σ(I): 16.986
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Num. unique all: 746 / Χ2: 1.016 / % possible all: 88.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0067refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.41 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.022 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 377 4.6 %RANDOM
Rwork0.198 ---
obs0.201 8174 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.06 Å2 / Biso mean: 10.419 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20.66 Å2
2---1.48 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms627 0 0 66 693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022633
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.99855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.675578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.13824.11834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56815127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8131510
X-RAY DIFFRACTIONr_chiral_restr0.1230.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02466
X-RAY DIFFRACTIONr_mcbond_it1.1141.5395
X-RAY DIFFRACTIONr_mcangle_it2.0222641
X-RAY DIFFRACTIONr_scbond_it3.4433238
X-RAY DIFFRACTIONr_scangle_it5.6554.5213
LS refinement shellResolution: 1.7→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 17 -
Rwork0.187 498 -
all-515 -
obs--84.01 %
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)
13.40611.9691-5.81022.1873-3.800910.09730.0322-0.1175-0.05710.1163-0.1274-0.0568-0.14850.21720.09520.0624-0.01870.05980.10080.0103-0.09720.7674.4345.022
21.3672-0.5494-3.7110.4610.379915.21370.03060.0715-0.03590.0028-0.03060.13420.0524-0.059400.0680.00320.09220.0032-0.0013-0.054813.4668.3371.764
35.1080.5259-5.8520.3993-0.48687.57520.07230.04610.04030.037-0.03620.0353-0.0758-0.017-0.03610.091-0.00580.10730.0153-0.0066-0.057114.055-1.2451.48
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 31
2X-RAY DIFFRACTION2B8 - 31
3X-RAY DIFFRACTION3C6 - 23

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