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- PDB-7siz: C-type inactivation in a voltage gated K+ channel -

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Basic information

Entry
Database: PDB / ID: 7siz
TitleC-type inactivation in a voltage gated K+ channel
Components
  • Voltage gated potassium channel Kv1.2-Kv2.1
  • Voltage-gated potassium channel subunit beta-2
KeywordsTRANSPORT PROTEIN / OXIDOREDUCTASE / Voltage gated ion channel / C- type inactivation / Beta subunit
Function / homology
Function and homology information


pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / 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 ...pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / 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 / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / regulation of potassium ion transmembrane transport / myoblast differentiation / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / 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 / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsReddi, R. / Riederer, E.A. / Matulef, K. / Whorton, M.R. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087546 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for C-type inactivation in a Shaker family voltage-gated K + channel.
Authors: Reddi, R. / Matulef, K. / Riederer, E.A. / Whorton, M.R. / Valiyaveetil, F.I.
History
DepositionOct 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
B: Voltage gated potassium channel Kv1.2-Kv2.1
C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,30518
Polymers192,3494
Non-polymers1,95614
Water68538
1
A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,61136
Polymers384,6998
Non-polymers3,91228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area34900 Å2
ΔGint-190 kcal/mol
Surface area113000 Å2
MethodPISA
2
C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

C: Voltage-gated potassium channel subunit beta-2
D: Voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,61136
Polymers384,6998
Non-polymers3,91228
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
Buried area34590 Å2
ΔGint-173 kcal/mol
Surface area113740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.732, 130.732, 278.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11B-501-

K

21B-502-

K

31B-503-

K

41B-504-

K

51B-505-

K

61B-506-

K

71D-501-

K

81D-502-

K

91D-503-

K

101D-504-

K

111D-505-

K

121D-506-

K

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Components

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


Mass: 37353.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Production host: Komagataella pastoris (fungus)
References: UniProt: P62483, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein Voltage gated potassium channel Kv1.2-Kv2.1


Mass: 58821.648 Da / Num. of mol.: 2
Mutation: L15H, C31S, C32S, N207Q, W362F, S367T, C435S, C482S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Komagataella pastoris (fungus)
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 50 mM Tris, pH 8.6, 28-30% PEG400, 8 mM CHAPS / PH range: 8.3-8.7

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→47.75 Å / Num. obs: 46801 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 78.59 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.07 / Net I/σ(I): 10.1
Reflection shellResolution: 3.1→3.22 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4607 / CC1/2: 0.35 / Rpim(I) all: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R9R

2r9r


Resolution: 3.1→47.75 Å / SU ML: 0.4623 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.8866 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2648 2374 5.07 %
Rwork0.2356 44427 -
obs0.2371 46801 89.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.94 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 0 108 38 10688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005710889
X-RAY DIFFRACTIONf_angle_d0.599614752
X-RAY DIFFRACTIONf_chiral_restr0.04041641
X-RAY DIFFRACTIONf_plane_restr0.00351851
X-RAY DIFFRACTIONf_dihedral_angle_d14.6633974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.140.40541270.39892194X-RAY DIFFRACTION76.7
3.14-3.220.40591070.35212289X-RAY DIFFRACTION80
3.22-3.310.38931240.3182400X-RAY DIFFRACTION83.47
3.31-3.410.30731570.27262463X-RAY DIFFRACTION87.28
3.41-3.520.26271090.26612564X-RAY DIFFRACTION88.13
3.52-3.640.26421480.22932649X-RAY DIFFRACTION92.22
3.64-3.790.25861510.21762669X-RAY DIFFRACTION93.59
3.79-3.960.2281540.2032761X-RAY DIFFRACTION95.67
3.96-4.170.22671610.20142796X-RAY DIFFRACTION97.05
4.17-4.430.23231610.1852833X-RAY DIFFRACTION98.2
4.43-4.770.2261380.17662903X-RAY DIFFRACTION99.06
4.77-5.250.2191480.19062918X-RAY DIFFRACTION98.84
5.25-6.010.26181560.22132924X-RAY DIFFRACTION99.29
6.01-7.560.27011650.25722968X-RAY DIFFRACTION99.3
7.56-47.750.2531630.23923164X-RAY DIFFRACTION98.93

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