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- PDB-3eb3: Voltage-dependent K+ channel beta subunit (W121A) in complex with... -

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Basic information

Entry
Database: PDB / ID: 3eb3
TitleVoltage-dependent K+ channel beta subunit (W121A) in complex with cortisone
ComponentsVoltage-gated potassium channel subunit beta-2
KeywordsTRANSPORT PROTEIN / oxidoreductase / kvbeta / cortisone / interface / Cytoplasm / Ion transport / Ionic channel / NADP / Phosphoprotein / Potassium / Potassium transport / Transport / Voltage-gated channel
Function / homology
Function and homology information


pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport ...pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / myoblast differentiation / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / axon terminus / voltage-gated potassium channel complex / extrinsic component of cytoplasmic side of plasma membrane / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton / neuron projection / axon / glutamatergic synapse / protein-containing complex binding / membrane / cytosol
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, Y. / Weng, J. / Kabaleeswaran, V. / Li, H. / Cao, Y. / Bhosle, R.C. / Zhou, M.
Citation
Journal: Nat.Chem.Biol. / Year: 2008
Title: Cortisone dissociates the Shaker family K+ channels from their beta subunits.
Authors: Pan, Y. / Weng, J. / Kabaleeswaran, V. / Li, H. / Cao, Y. / Bhosle, R.C. / Zhou, M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of a voltage-dependent K+ channel beta subunit.
Authors: Gulbis, J.M. / Mann, S. / MacKinnon, R.
#2: Journal: 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
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Voltage-gated potassium channel subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5613
Polymers36,4571
Non-polymers1,1042
Water2,414134
1
A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,24412
Polymers145,8284
Non-polymers4,4158
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 area12370 Å2
ΔGint-31 kcal/mol
Surface area51200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.198, 113.198, 146.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Voltage-gated potassium channel subunit beta-2 / / K(+) channel subunit beta-2 / Kv-beta-2


Mass: 36457.059 Da / Num. of mol.: 1 / Fragment: cytoplasmic Kvbeta subunit / Mutation: W121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / References: UniProt: P62483
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PDN / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / PREDNISONE / 1,4 PREGNADIENE-17ALPHA,21-DIOL-3,11,20-TRIONE / 1-CORTISONE / DEHYDROCORTISONE / Prednisone


Mass: 358.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26O5 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6-15% glycerol, 1.5 M ammonium sulfate, 0.1 M Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 7.9 - 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2007
RadiationMonochromator: SAGITALLY FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32564 / % possible obs: 99 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.04 / Net I/σ(I): 52.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 9.3 / Num. unique all: 3197 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1EXB, chain A, beta subunit

1exb


Resolution: 2→44.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3291792.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1628 5.1 %RANDOM
Rwork0.222 ---
obs0.222 32159 99 %-
all-32564 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9253 Å2 / ksol: 0.357414 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---1.03 Å20 Å2
3---2.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 74 134 2757
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.961.5
X-RAY DIFFRACTIONc_mcangle_it2.972
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 257 4.8 %
Rwork0.261 5055 -
obs-3197 99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2crx.paramcrx.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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