7WF4

Composite map of human Kv1.3 channel in dalazatide-bound state with beta subunits


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Rearrangement of a unique Kv1.3 selectivity filter conformation upon binding of a drug.

Tyagi, 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.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2113536119
  • Primary Citation of Related Structures:  
    7WF3, 7WF4

  • PubMed 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 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.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore 637551.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily A member 3A [auth D],
J [auth B],
K [auth F],
L [auth H]
283Homo sapiensMutation(s): 0 
Gene Names: KCNA3HGK5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P22001 (Homo sapiens)
Explore P22001 
Go to UniProtKB:  P22001
PHAROS:  P22001
GTEx:  ENSG00000177272 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22001
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-gated potassium channel subunit beta-2B [auth G],
C [auth I],
E [auth M],
I [auth o]
328Homo sapiensMutation(s): 0 
Gene Names: KCNAB2KCNA2BKCNK2
EC: 1.1.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13303 (Homo sapiens)
Explore Q13303 
Go to UniProtKB:  Q13303
PHAROS:  Q13303
GTEx:  ENSG00000069424 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13303
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily A member 3D [auth J],
F [auth N],
G [auth O],
H [auth P]
106Homo sapiensMutation(s): 0 
Gene Names: KCNA3HGK5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P22001 (Homo sapiens)
Explore P22001 
Go to UniProtKB:  P22001
PHAROS:  P22001
GTEx:  ENSG00000177272 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22001
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
M [auth G],
N [auth I],
O [auth M],
P [auth o]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
Q [auth B],
R [auth B],
S [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeMOE2017-T2-2-089, MOE2020-T1-002-059, MOE2016-T2-2-032

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 2.0: 2022-05-25
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Structure summary