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- PDB-1dsx: KV1.2 T1 DOMAIN, RESIDUES 33-119, T46V MUTANT -

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Basic information

Entry
Database: PDB / ID: 1dsx
TitleKV1.2 T1 DOMAIN, RESIDUES 33-119, T46V MUTANT
ComponentsPROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
KeywordsSIGNALING PROTEIN / VOLTAGE-GATED POTASSIUM CHANNEL / ASSEMBLY DOMAIN / TETRAMER
Function / homology
Function and homology information


optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / axon initial segment / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / axon initial segment / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / juxtaparanode region of axon / optic nerve development / neuronal cell body membrane / regulation of dopamine secretion / action potential / kinesin binding / lamellipodium membrane / calyx of Held / voltage-gated potassium channel activity / neuronal action potential / voltage-gated potassium channel complex / axon terminus / sensory perception of pain / potassium ion transmembrane transport / protein homooligomerization / cerebral cortex development / lamellipodium / presynaptic membrane / perikaryon / postsynaptic membrane / endosome / axon / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / 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 / SYNCHROTRON / Resolution: 1.6 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
DepositionJan 10, 2000Deposition 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 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,9688
Polymers83,9688
Non-polymers00
Water9,926551
1
A: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
B: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
C: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
D: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)


Theoretical massNumber of molelcules
Total (without water)41,9844
Polymers41,9844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
F: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
G: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
H: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)


Theoretical massNumber of molelcules
Total (without water)41,9844
Polymers41,9844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.390, 78.398, 126.924
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
PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)


Mass: 10495.991 Da / Num. of mol.: 8 / Fragment: N-TERMINAL ASSEMBLY DOMAIN, RESIDUES 33-119 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PET24 / Production host: Escherichia coli (E. coli) / References: UniProt: P63142
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growpH: 8.5
Details: 22% PEG 1500, 5 % ISOPROPANOL, 200 MM NA ACETATE, 12 MM SRCL2, 50 MM TRIS, PH 8.5, pH 8.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
222 %PEG15001reservoir
35 %isopropanol1reservoir
4200 mM1reservoirNaC2H3O2
512 mM1reservoirSrCl2
650 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Aug 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 97159 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.75 Å / Rmerge(I) obs: 0.371 / % possible all: 84.4
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 23.1 Å2

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.279 9715 RANDOM
Rwork0.237 --
obs-97159 -
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5944 0 0 555 6499
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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