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- PDB-1exb: STRUCTURE OF THE CYTOPLASMIC BETA SUBUNIT-T1 ASSEMBLY OF VOLTAGE-... -

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Basic information

Entry
Database: PDB / ID: 1exb
TitleSTRUCTURE OF THE CYTOPLASMIC BETA SUBUNIT-T1 ASSEMBLY OF VOLTAGE-DEPENDENT K CHANNELS
Components
  • KV BETA2 PROTEIN
  • POTASSIUM CHANNEL KV1.1
KeywordsMETAL TRANSPORT / ion channel / oxidoreductase / beta subunit
Function / homology
Function and homology information


neuronal signal transduction / pinceau fiber / regulation of action potential / cell communication by electrical coupling / detection of mechanical stimulus involved in sensory perception of touch / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / membrane repolarization during action potential ...neuronal signal transduction / pinceau fiber / regulation of action potential / cell communication by electrical coupling / detection of mechanical stimulus involved in sensory perception of touch / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / membrane repolarization during action potential / magnesium ion homeostasis / NADPH oxidation / regulation of muscle contraction / regulation of protein localization to cell surface / axon initial segment / corpus callosum development / paranode region of axon / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / aldo-keto reductase (NADPH) activity / delayed rectifier potassium channel activity / cellular response to magnesium ion / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / regulation of potassium ion transmembrane transport / myoblast differentiation / anchoring junction / Neutrophil degranulation / neuromuscular process / optic nerve development / axon development / startle response / action potential / calyx of Held / voltage-gated potassium channel activity / neuroblast proliferation / neuronal action potential / potassium channel regulator activity / hematopoietic progenitor cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / voltage-gated potassium channel complex / axon terminus / potassium ion transmembrane transport / regulation of membrane potential / hippocampus development / postsynaptic density membrane / brain development / protein homooligomerization / cerebral cortex development / cytoplasmic side of plasma membrane / disordered domain specific binding / protein localization / cell junction / presynaptic membrane / cytoplasmic vesicle / perikaryon / postsynaptic membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton / neuron projection / apical plasma membrane / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / cell surface / endoplasmic reticulum / membrane / plasma membrane / cytosol
Similarity search - Function
Potassium channel, voltage dependent, Kv1.1 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / 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 ...Potassium channel, voltage dependent, Kv1.1 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / 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 / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / 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 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Potassium voltage-gated channel subfamily A member 1 / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsGulbis, J.M. / Zhou, M. / Mann, S. / MacKinnon, R.
CitationJournal: Science / Year: 2000
Title: Structure of the cytoplasmic beta subunit-T1 assembly of voltage-dependent K+ channels.
Authors: Gulbis, J.M. / Zhou, M. / Mann, S. / MacKinnon, R.
History
DepositionMay 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs ..._refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 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

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Assembly

Deposited unit
A: KV BETA2 PROTEIN
E: POTASSIUM CHANNEL KV1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3143
Polymers49,5692
Non-polymers7451
Water4,792266
1
A: KV BETA2 PROTEIN
E: POTASSIUM CHANNEL KV1.1
hetero molecules

A: KV BETA2 PROTEIN
E: POTASSIUM CHANNEL KV1.1
hetero molecules

A: KV BETA2 PROTEIN
E: POTASSIUM CHANNEL KV1.1
hetero molecules

A: KV BETA2 PROTEIN
E: POTASSIUM CHANNEL KV1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,25712
Polymers198,2758
Non-polymers2,9824
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)100.725, 100.725, 110.901
Angle α, β, γ (deg.)90, 90, 90
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a heterooctamer (t1)4(beta)4 constructed by the operation of the crystallographic 4-fold on both chains (A and E)

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Components

#1: Protein KV BETA2 PROTEIN


Mass: 37221.887 Da / Num. of mol.: 1 / Fragment: BETA SUBUNIT, RESIDUES 36-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PFASTBAC1 / Production host: unidentified baculovirus / References: UniProt: P62483
#2: Protein POTASSIUM CHANNEL KV1.1


Mass: 12346.951 Da / Num. of mol.: 1 / Fragment: T1 DOMAIN, RESIDUES 27-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PACG2T / Production host: unidentified baculovirus / References: UniProt: P10499
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: Peg 4000, glycine, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMglycine1reservoir
36 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 33907 / Num. obs: 33500 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 9689 % / Rmerge(I) obs: 0.3 / Num. unique all: 2064 / % possible all: 92.9
Reflection shell
*PLUS
% possible obs: 92.9 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→40 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1647 4.9 %random
Rwork0.215 ---
all0.216 33962 --
obs0.216 33453 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 48 266 3628
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.8

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