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- PDB-7wf3: Composite map of human Kv1.3 channel in apo state with beta subunits -

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Basic information

Entry
Database: PDB / ID: 7wf3
TitleComposite map of human Kv1.3 channel in apo state with beta subunits
Components
  • (Potassium voltage-gated channel subfamily A member ...) x 2
  • Voltage-gated potassium channel subunit beta-2
KeywordsMEMBRANE PROTEIN / Ion channel / Kv channel / Potassium channel / Peptide toxin / ShK / Dalazatide / Selectivity filter / Molecular dynamics simulation
Function / homology
Function and homology information


pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / regulation of protein localization to cell surface / voltage-gated monoatomic ion channel activity / : / delayed rectifier potassium channel 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 / methylglyoxal reductase (NADPH) (acetol producing) activity / regulation of protein localization to cell surface / voltage-gated monoatomic ion channel activity / : / delayed rectifier potassium channel 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 / action potential / voltage-gated potassium channel activity / potassium channel regulator activity / specific granule membrane / voltage-gated potassium channel complex / potassium ion transmembrane transport / protein homooligomerization / potassium ion transport / cytoplasmic side of plasma membrane / transmembrane transporter binding / cytoskeleton / axon / synapse / Neutrophil degranulation / perinuclear region of cytoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Potassium channel, voltage dependent, Kv1.3 / 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, Kv1.3 / 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 / Helix Hairpins - #70 / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Potassium voltage-gated channel subfamily A member 3 / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTyagi, A. / Ahmed, T. / Jian, S. / Bajaj, S. / Ong, S.T. / Goay, S.S.M. / Zhao, Y. / Vorobyov, I. / Tian, C. / Chandy, K.G. / Bhushan, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2017-T2-2-089, MOE2020-T1-002-059, MOE2016-T2-2-032 Singapore
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Rearrangement of a unique Kv1.3 selectivity filter conformation upon binding of a drug.
Authors: Anu Tyagi / Tofayel Ahmed / Shi Jian / Saumya Bajaj / Seow Theng Ong / Stephanie Shee Min Goay / Yue Zhao / Igor Vorobyov / Changlin Tian / K George Chandy / Shashi Bhushan /
Abstract: We report two structures of the human voltage-gated potassium channel (Kv) Kv1.3 in immune cells alone (apo-Kv1.3) and bound to an immunomodulatory drug called dalazatide (dalazatide-Kv1.3). Both the ...We report two structures of the human voltage-gated potassium channel (Kv) Kv1.3 in immune cells alone (apo-Kv1.3) and bound to an immunomodulatory drug called dalazatide (dalazatide-Kv1.3). Both the apo-Kv1.3 and dalazatide-Kv1.3 structures are in an activated state based on their depolarized voltage sensor and open inner gate. In apo-Kv1.3, the aromatic residue in the signature sequence (Y447) adopts a position that diverges 11 Å from other K channels. The outer pore is significantly rearranged, causing widening of the selectivity filter and perturbation of ion binding within the filter. This conformation is stabilized by a network of intrasubunit hydrogen bonds. In dalazatide-Kv1.3, binding of dalazatide to the channel's outer vestibule narrows the selectivity filter, Y447 occupies a position seen in other K channels, and this conformation is stabilized by a network of intersubunit hydrogen bonds. These remarkable rearrangements in the selectivity filter underlie Kv1.3's transition into the drug-blocked state.
History
DepositionDec 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 2.0May 25, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_fragment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.pdbx_end_seq_num / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_asym.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 2.2Nov 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: em_admin / em_entity_assembly_molwt ...em_admin / em_entity_assembly_molwt / em_entity_assembly_naturalsource / em_entity_assembly_recombinant
Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
B: Potassium voltage-gated channel subfamily A member 3
C: Voltage-gated potassium channel subunit beta-2
D: Potassium voltage-gated channel subfamily A member 3
F: Potassium voltage-gated channel subfamily A member 3
G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 3
I: Voltage-gated potassium channel subunit beta-2
J: Potassium voltage-gated channel subfamily A member 3
M: Voltage-gated potassium channel subunit beta-2
N: Potassium voltage-gated channel subfamily A member 3
O: Potassium voltage-gated channel subfamily A member 3
P: Potassium voltage-gated channel subfamily A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,04820
Polymers324,91812
Non-polymers3,1308
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Potassium voltage-gated channel subfamily A member ... , 2 types, 8 molecules BDFHJNOP

#1: Protein
Potassium voltage-gated channel subfamily A member 3 / HGK5 / HLK3 / HPCN3 / Voltage-gated K(+) channel HuKIII / Voltage-gated potassium channel subunit Kv1.3


Mass: 31747.734 Da / Num. of mol.: 4 / Fragment: TM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNA3, HGK5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22001
#3: Protein
Potassium voltage-gated channel subfamily A member 3 / HGK5 / HLK3 / HPCN3 / Voltage-gated K(+) channel HuKIII / Voltage-gated potassium channel subunit Kv1.3


Mass: 12777.475 Da / Num. of mol.: 4 / Fragment: T1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNA3, HGK5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22001

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Protein , 1 types, 4 molecules CGIM

#2: Protein
Voltage-gated potassium channel subunit beta-2 / K(+) channel subunit beta-2 / Kv-beta-2 / hKvbeta2


Mass: 36704.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNAB2, KCNA2B, KCNK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13303, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 3 types, 124 molecules

#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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Composite map of human Kv1.3 channel in apo state with beta subunitsCOMPLEX#1-#30RECOMBINANT
2TM domain focused map of human Kv1.3COMPLEX#31RECOMBINANT
3Soluble domain focused map of human Kv1.3COMPLEX#1-#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera (butterflies/moths)7106
23Spodoptera (butterflies/moths)7106
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177130
Details: The above mentioned 3.4 Ang resolution was obtained for TM domain after application of C4 symmetry. The soluble domain map (another map deposited here) was resolved to 2.9 Ang.
Symmetry type: POINT

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