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- PDB-1zsx: Crystal Structure Of Human Potassium Channel Kv Beta-subunit (KCNAB2) -

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Basic information

Entry
Database: PDB / ID: 1zsx
TitleCrystal Structure Of Human Potassium Channel Kv Beta-subunit (KCNAB2)
ComponentsVoltage-gated potassium channel beta-2 subunit
KeywordsOXIDOREDUCTASE / Potassium Channel / Kv Beta-subunit / human / aldo-keto reductase / Structural Genomics / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / NADPH oxidation / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / Voltage gated Potassium channels / 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 ...pinceau fiber / regulation of action potential / methylglyoxal reductase (NADPH) (acetol producing) activity / NADPH oxidation / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / Voltage gated Potassium channels / 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 / tertiary granule membrane / voltage-gated potassium channel activity / potassium channel regulator activity / specific granule membrane / voltage-gated potassium channel complex / cytoplasmic side of plasma membrane / transmembrane transporter binding / cytoskeleton / Neutrophil degranulation / synapse / membrane / plasma 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWennerstrand, P. / Johannsson, I. / Ugochukwu, E. / Kavanagh, K. / Edwards, A. / Arrowsmith, C. / Williams, L. / Sundstrom, M. / Guo, K. / von Delft, F. ...Wennerstrand, P. / Johannsson, I. / Ugochukwu, E. / Kavanagh, K. / Edwards, A. / Arrowsmith, C. / Williams, L. / Sundstrom, M. / Guo, K. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure Of Human Potassium Channel Kv Beta-subunit (KCNAB2)
Authors: Wennerstrand, P. / Johannsson, I. / Ugochukwu, E. / Kavanagh, K. / Edwards, A. / Arrowsmith, C. / Williams, L. / Sundstrom, M. / Guo, K. / von Delft, F. / Oppermann, U.
History
DepositionMay 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,7876
Polymers38,9021
Non-polymers8855
Water3,837213
1
A: Voltage-gated potassium channel beta-2 subunit
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)159,14724
Polymers155,6064
Non-polymers3,54120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15230 Å2
ΔGint-246 kcal/mol
Surface area45100 Å2
MethodPISA
2
A: Voltage-gated potassium channel beta-2 subunit
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)318,29448
Polymers311,2138
Non-polymers7,08240
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area32940 Å2
ΔGint-334 kcal/mol
Surface area86730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.231, 113.231, 142.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-855-

HOH

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Components

#1: Protein Voltage-gated potassium channel beta-2 subunit / K+ / channel beta-2 subunit / Kv-beta-2 / HKvbeta2 / AKR6A5


Mass: 38901.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Origene / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q13303
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.9 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG300, sodium/potassium phosphate, sodium chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→44.3 Å / Num. obs: 36582 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QRQ.pdb

1qrq


Resolution: 1.9→44.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.821 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1724 1831 5 %RANDOM
Rwork0.14478 ---
all0.14623 34746 --
obs0.14623 34746 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.597 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2---1.57 Å20 Å2
3---3.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 52 213 2750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222631
X-RAY DIFFRACTIONr_bond_other_d0.0010.022418
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9793582
X-RAY DIFFRACTIONr_angle_other_deg0.85635607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3545336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32923.585106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19915452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6781518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022904
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_nbd_refined0.210.2576
X-RAY DIFFRACTIONr_nbd_other0.1840.22524
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21349
X-RAY DIFFRACTIONr_nbtor_other0.0890.21529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.219
X-RAY DIFFRACTIONr_mcbond_it3.00621743
X-RAY DIFFRACTIONr_mcbond_other0.892671
X-RAY DIFFRACTIONr_mcangle_it3.49832602
X-RAY DIFFRACTIONr_scbond_it5.24441136
X-RAY DIFFRACTIONr_scangle_it6.9826973
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 127 -
Rwork0.209 2506 -
obs--97.7 %
Refinement TLS params.Method: refined / Origin x: 7.0447 Å / Origin y: -30.3171 Å / Origin z: 19.233 Å
111213212223313233
T-0.0453 Å20.0026 Å20.002 Å2--0.0707 Å20.0139 Å2---0.0737 Å2
L0.6926 °2-0.1098 °20.0705 °2-1.2308 °2-0.3494 °2--0.7111 °2
S0.0049 Å °0.0074 Å °-0.1551 Å °-0.0919 Å °-0.0177 Å °-0.1064 Å °0.1142 Å °0.0046 Å °0.0127 Å °

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