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- PDB-3bj4: The KCNQ1 (Kv7.1) C-terminus, a multi-tiered scaffold for subunit... -

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Basic information

Entry
Database: PDB / ID: 3bj4
TitleThe KCNQ1 (Kv7.1) C-terminus, a multi-tiered scaffold for subunit assembly and protein interaction
ComponentsPotassium voltage-gated channel subfamily KQT member 1
KeywordsSIGNALING PROTEIN / Coiled coil / Alternative splicing / 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 / regulation of heart rate by cardiac conduction / social behavior / 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 / erythrocyte differentiation / cytoplasmic vesicle membrane / 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
NICKEL (II) ION / Potassium voltage-gated channel subfamily KQT member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsWiener, R. / Hirsch, J.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The KCNQ1 (Kv7.1) COOH terminus, a multitiered scaffold for subunit assembly and protein interaction.
Authors: Wiener, R. / Haitin, Y. / Shamgar, L. / Fernandez-Alonso, M.C. / Martos, A. / Chomsky-Hecht, O. / Rivas, G. / Attali, B. / Hirsch, J.A.
History
DepositionDec 3, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9073
Polymers10,8482
Non-polymers591
Water95553
1
A: Potassium voltage-gated channel subfamily KQT member 1
B: Potassium voltage-gated channel subfamily KQT member 1
hetero molecules

A: Potassium voltage-gated channel subfamily KQT member 1
B: Potassium voltage-gated channel subfamily KQT member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8146
Polymers21,6974
Non-polymers1172
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7270 Å2
ΔGint-73 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.321, 51.321, 71.094
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
11A-1-

NI

21B-632-

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: 5424.181 Da / Num. of mol.: 2 / Fragment: C-terminal Helix D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ1 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: P51787
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12-16% PEG 8K, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 7656 / Num. obs: 7656 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.065 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.36 / Num. unique all: 1432 / Rsym value: 0.33 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→44.46 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.985 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.177 / ESU R Free: 0.16
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25492 354 4.6 %RANDOM
Rwork0.22149 ---
obs0.22308 7283 99.28 %-
all-7336 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.29 Å20 Å2
2---0.59 Å20 Å2
3---0.88 Å2
Refine analyzeLuzzati coordinate error free: 0.16 Å
Refinement stepCycle: LAST / Resolution: 2→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms640 0 1 53 694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021647
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.969877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.35586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.31324.83931
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19415126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.943156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02482
X-RAY DIFFRACTIONr_nbd_refined0.1870.2312
X-RAY DIFFRACTIONr_nbtor_refined0.2730.2458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.28
X-RAY DIFFRACTIONr_mcbond_it1.8453422
X-RAY DIFFRACTIONr_mcangle_it2.7125662
X-RAY DIFFRACTIONr_scbond_it5.0347236
X-RAY DIFFRACTIONr_scangle_it6.83810215
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 30 -
Rwork0.306 528 -
obs--98.76 %

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