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- PDB-7sit: Crystal structure of Voltage gated potassium ion channel, Kv 1.2 ... -

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Basic information

Entry
Database: PDB / ID: 7sit
TitleCrystal structure of Voltage gated potassium ion channel, Kv 1.2 chimera-3m
Components
  • Voltage gated potassium channel Kv1.2-Kv2.1
  • Voltage-gated potassium channel subunit beta-2
KeywordsTRANSPORT PROTEIN / OXIDOREDUCTASE / Ion channel / C-type inactivation / Voltage gated Potassium ion channel / Chimera
Function / homology
Function and homology information


pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / regulation of protein localization to cell surface / : / axon initial segment / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / myoblast differentiation ...pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / regulation of protein localization to cell surface / : / axon initial segment / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / myoblast differentiation / regulation of potassium ion transmembrane transport / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / axon terminus / voltage-gated potassium channel complex / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / cytoskeleton / neuron projection / postsynaptic density / axon / protein-containing complex binding / glutamatergic synapse / 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 / OXYGEN ATOM / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.32 Å
AuthorsReddi, R. / Matulef, K. / Riederer, E.A. / 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 14, 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)194,01311
Polymers192,3534
Non-polymers1,6597
Water00
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)388,05724
Polymers384,7078
Non-polymers3,35016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area35550 Å2
ΔGint-167 kcal/mol
Surface area110090 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)387,99320
Polymers384,7078
Non-polymers3,28612
Water0
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 area35470 Å2
ΔGint-158 kcal/mol
Surface area109570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.587, 129.587, 278.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-501-

K

21B-502-

K

31B-503-

O

41D-501-

K

51D-502-

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: 58823.617 Da / Num. of mol.: 2
Mutation: L15H, C31S, C32S, N207Q, W362F, S367T, V377T, 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.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
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 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris, pH 8.5, 28-32% PEG400, CHAPS / PH range: 8.3-8.8

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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: Mar 5, 2020
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.32→49.16 Å / Num. obs: 35720 / % possible obs: 99.9 % / Redundancy: 14.9 % / CC1/2: 0.99 / CC star: 0.54 / Net I/σ(I): 7.2
Reflection shellResolution: 3.32→3.51 Å / Num. unique obs: 4588 / CC1/2: 0.54

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R9R

2r9r


Resolution: 3.32→49.159 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2893 1818 5.09 %
Rwork0.2509 33902 -
obs0.2529 35720 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 299.21 Å2 / Biso mean: 126.359 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.32→49.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10341 0 101 0 10442
Biso mean--62.41 --
Num. residues----1300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3201-3.40980.34471380.36248997
3.4098-3.51010.42391180.3576253198
3.5101-3.62340.39941410.3532255699
3.6234-3.75290.34751420.31122548100
3.7529-3.90310.33421360.2842257599
3.9031-4.08060.27321540.25342560100
4.0806-4.29560.31091370.22232586100
4.2956-4.56460.28261480.20942603100
4.5646-4.91670.22951340.19732614100
4.9167-5.4110.24041230.20142654100
5.411-6.19260.24891460.23352650100
6.1926-7.7970.27221480.25782676100
7.797-49.150.2931530.2544286099

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