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- PDB-1qdw: N-TERMINAL DOMAIN, VOLTAGE-GATED POTASSIUM CHANNEL KV1.2 RESIDUES... -

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Basic information

Entry
Database: PDB / ID: 1qdw
TitleN-TERMINAL DOMAIN, VOLTAGE-GATED POTASSIUM CHANNEL KV1.2 RESIDUES 33-119
ComponentsKV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
KeywordsSIGNALING PROTEIN / VOLTAGE-GATED POTASSIUM CHANNEL / TETRAMERIZATION DOMAIN / INTRACELLULAR GATE / TETRAMER
Function / homology
Function and homology information


optic nerve structural organization / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity ...optic nerve structural organization / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / axon initial segment / optic nerve development / juxtaparanode region of axon / outward rectifier potassium channel activity / neuronal cell body membrane / regulation of dopamine secretion / lamellipodium membrane / action potential / kinesin binding / voltage-gated potassium channel activity / neuronal action potential / axon terminus / voltage-gated potassium channel complex / potassium ion transmembrane transport / sensory perception of pain / calyx of Held / protein homooligomerization / cerebral cortex development / lamellipodium / presynaptic membrane / perikaryon / postsynaptic membrane / endosome / axon / dendrite / endoplasmic reticulum membrane / glutamatergic synapse / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily ...Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily A member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMinor Jr., D.L. / Lin, Y.-F. / Mobley, B.C. / Avelar, A. / Jan, Y.N. / Jan, L.Y. / Berger, J.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: The polar T1 interface is linked to conformational changes that open the voltage-gated potassium channel.
Authors: Minor, D.L. / Lin, Y.F. / Mobley, B.C. / Avelar, A. / Jan, Y.N. / Jan, L.Y. / Berger, J.M.
History
DepositionJul 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
B: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
C: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
D: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
E: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
F: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
G: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
H: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)83,9848
Polymers83,9848
Non-polymers00
Water9,710539
1
A: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
B: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
C: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
D: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)41,9924
Polymers41,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
F: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
G: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
H: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)41,9924
Polymers41,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.260, 78.740, 125.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL


Mass: 10497.965 Da / Num. of mol.: 8 / Fragment: N-TERMINAL DOMAIN KV1.2, RESIDUES 33-119 (CORE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / References: UniProt: P63142
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG 1500, 5% N-PROPANOL, 120 MM GDHCL 50 MM MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
29 %PEG15001reservoir
35 %n-propanol1reservoir
4120 mMGdm HCl1reservoir
550 mMMES1reservoir
60-15 %water1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 42293 / % possible obs: 94.9 % / Redundancy: 14.6 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.285 / % possible all: 83.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % possible obs: 94.5 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Rmerge(I) obs: 0.283

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.266 3531 RANDOM
Rwork0.223 --
obs0.223 42293 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 0 539 6491
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.13

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