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- PDB-2ovc: Crystal structure of a coiled-coil tetramerization domain from Kv... -

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Basic information

Entry
Database: PDB / ID: 2ovc
TitleCrystal structure of a coiled-coil tetramerization domain from Kv7.4 channels
ComponentsPotassium voltage-gated channel subfamily KQT member 4
KeywordsTRANSPORT PROTEIN / Voltage-gated channel / Potassium channel / Ion channel assembly / Coiled-coil / Tetramer
Function / homology
Function and homology information


Voltage gated Potassium channels / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / voltage-gated potassium channel activity / potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / basal plasma membrane / sensory perception of sound ...Voltage gated Potassium channels / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / voltage-gated potassium channel activity / potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / basal plasma membrane / sensory perception of sound / potassium ion transport / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily KQT member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsHoward, R.J. / Clark, K.A. / Holton, J.M. / Minor, D.L.
CitationJournal: Neuron / Year: 2007
Title: Structural Insight into KCNQ (Kv7) Channel Assembly and Channelopathy.
Authors: Howard, R.J. / Clark, K.A. / Holton, J.M. / Minor, D.L.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.5Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 4


Theoretical massNumber of molelcules
Total (without water)3,7381
Polymers3,7381
Non-polymers00
Water32418
1
A: Potassium voltage-gated channel subfamily KQT member 4

A: Potassium voltage-gated channel subfamily KQT member 4

A: Potassium voltage-gated channel subfamily KQT member 4

A: Potassium voltage-gated channel subfamily KQT member 4


Theoretical massNumber of molelcules
Total (without water)14,9544
Polymers14,9544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area6090 Å2
ΔGint-53 kcal/mol
Surface area6890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)33.185, 33.185, 55.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: y, 1-x, z; 1-x, 1-y, z; and 1-y, x, z

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Components

#1: Protein/peptide Potassium voltage-gated channel subfamily KQT member 4 / Voltage-gated potassium channel subunit Kv7.4 / Potassium channel subunit alpha KvLQT4 / KQT-like 4


Mass: 3738.399 Da / Num. of mol.: 1 / Fragment: coiled-coil assembly domain, residues 611-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ4 / Plasmid: pSV272 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P56696
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 45% MPD, 0.2M ammonium acetate, 0.1M Bis-Tris, pH 5.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.116
2
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2005 / Details: Double Crystal
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.07→28.46 Å / Num. obs: 1841 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.053 / Χ2: 0.913 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.146.10.0961940.5041100
2.14-2.2370.0911840.5161100
2.23-2.337.40.0921690.5971100
2.33-2.457.60.0751950.6681100
2.45-2.617.40.0651760.8171100
2.61-2.817.60.0641880.9611100
2.81-3.097.50.0551771.1421100
3.09-3.547.50.0561871.5151100
3.54-4.467.50.041851.0881100
4.46-507.10.0431861.225195.9

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Phasing

Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→28.46 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.183 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 81 4.4 %RANDOM
Rwork0.196 ---
obs0.197 1841 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.07→28.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms245 0 0 18 263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022251
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.005334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.32825.45511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3031557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.443151
X-RAY DIFFRACTIONr_chiral_restr0.10.239
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02174
X-RAY DIFFRACTIONr_nbd_refined0.2240.293
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.29
X-RAY DIFFRACTIONr_mcbond_it0.8541.5155
X-RAY DIFFRACTIONr_mcangle_it1.5132242
X-RAY DIFFRACTIONr_scbond_it2.5653107
X-RAY DIFFRACTIONr_scangle_it4.5694.592
LS refinement shellResolution: 2.074→2.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 4 -
Rwork0.261 138 -
obs-142 95.95 %

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