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- PDB-7wf4: Composite map of human Kv1.3 channel in dalazatide-bound state wi... -

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Entry
Database: PDB / ID: 7wf4
TitleComposite map of human Kv1.3 channel in dalazatide-bound 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 / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / 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 / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / 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 / 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 / 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 / Author supporting evidence / 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_entity_instance_feature / 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_torsion / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity.formula_weight / _entity.pdbx_fragment ..._entity.formula_weight / _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_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _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_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _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: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 23, 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
D: Potassium voltage-gated channel subfamily A member 3
G: Voltage-gated potassium channel subunit beta-2
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
o: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 3
F: Potassium voltage-gated channel subfamily A member 3
H: Potassium voltage-gated channel subfamily A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,86019
Polymers323,76912
Non-polymers3,0917
Water1,802100
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 DBFHJNOP

#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: 31460.467 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 GIMo

#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, 107 molecules

#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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 dalazatide-bound state with beta subunitsCOMPLEX#1-#30RECOMBINANT
2TM domain focused map of human Kv1.3 channel bound to dalazatideCOMPLEX#21RECOMBINANT
3Focused map of human Kv1.3 channel T1 domains and beta 2.1 subunitsCOMPLEX#1, #31RECOMBINANT
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: 153218 / Symmetry type: POINT

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