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- PDB-5wie: Crystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant ... -

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Basic information

Entry
Database: PDB / ID: 5wie
TitleCrystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant in an inactivated state
Components
  • Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
  • Voltage-gated potassium channel subunit beta-2
KeywordsMEMBRANE PROTEIN / METAL TRANSPORT / Ion Channel / Inactivation / Voltage-gated
Function / homology
Function and homology information


Voltage gated Potassium channels / optic nerve structural organization / pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of circadian sleep/wake cycle, non-REM sleep / paranodal junction / potassium ion export across plasma membrane ...Voltage gated Potassium channels / optic nerve structural organization / pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of circadian sleep/wake cycle, non-REM sleep / paranodal junction / potassium ion export across plasma membrane / regulation of protein localization to cell surface / corpus callosum development / : / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / axon initial segment / optic nerve development / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / outward rectifier potassium channel activity / myoblast differentiation / regulation of potassium ion transmembrane transport / Neutrophil degranulation / neuronal cell body membrane / neuromuscular process / regulation of dopamine secretion / lamellipodium membrane / action potential / voltage-gated potassium channel activity / kinesin binding / potassium channel regulator activity / hematopoietic progenitor cell differentiation / neuronal action potential / voltage-gated potassium channel complex / axon terminus / potassium ion transmembrane transport / sensory perception of pain / calyx of Held / postsynaptic density membrane / protein homooligomerization / cerebral cortex development / cytoplasmic side of plasma membrane / lamellipodium / presynaptic membrane / perikaryon / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / endosome / neuron projection / postsynaptic density / axon / dendrite / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Potassium channel, voltage dependent, Kv1.2 / 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 / Voltage-gated potassium channels. Chain C / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel ...Potassium channel, voltage dependent, Kv1.2 / 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 / Voltage-gated potassium channels. Chain C / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / NADP-dependent oxidoreductase domain / Helix Hairpins - #70 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-PGW / Voltage-gated potassium channel subunit beta-2 / Potassium voltage-gated channel subfamily A member 2 / Potassium voltage-gated channel subfamily A member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPau, V. / Zhou, Y. / Ramu, Y. / Xu, Y. / Lu, Z.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM055560 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1DK109919 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Crystal structure of an inactivated mutant mammalian voltage-gated K(+) channel.
Authors: Pau, V. / Zhou, Y. / Ramu, Y. / Xu, Y. / Lu, Z.
History
DepositionJul 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,91020
Polymers195,6174
Non-polymers6,29416
Water00
1
A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,81348
Polymers391,2348
Non-polymers18,57940
Water0
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 area44340 Å2
ΔGint-46 kcal/mol
Surface area114700 Å2
MethodPISA
2
G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,82932
Polymers391,2348
Non-polymers6,59524
Water0
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 area37310 Å2
ΔGint-136 kcal/mol
Surface area106050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.124, 143.124, 284.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-506-

K

21B-507-

K

31B-508-

K

41B-509-

K

51H-502-

K

61H-503-

K

71H-504-

K

81H-505-

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 / Plasmid: pPICZ-C / Production host: Pichia (fungus)
References: UniProt: P62483, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2 / RAK / RBK2 / RCK5 / Voltage-gated potassium channel subunit Kv1.2 / MK2 / Voltage-gated potassium ...RAK / RBK2 / RCK5 / Voltage-gated potassium channel subunit Kv1.2 / MK2 / Voltage-gated potassium channel subunit Kv1.2


Mass: 60455.312 Da / Num. of mol.: 2 / Mutation: V406W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Gene: Kcna2 / Plasmid: pPICZ-C / Production host: Pichia (fungus) / References: UniProt: P63142, UniProt: P63141
#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-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K

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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: 3.72 Å3/Da / Density % sol: 73.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 50 mM Tris-Cl pH 8.3, 29-31% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 45103 / % possible obs: 99.5 % / Redundancy: 11.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.11 / Net I/σ(I): 7.9
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.604 / Rpim(I) all: 0.413 / % possible all: 97.2

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R9R

2r9r


Resolution: 3.3→40 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.243 -5 %
Rwork0.236 --
obs-45103 99.5 %
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10771 0 184 0 10955

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