5WIE | pdb_00005wie

Crystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant in an inactivated state

PDB DOI: https://doi.org/10.2210/pdb5WIE/pdb

Classification: MEMBRANE PROTEIN, METAL TRANSPORT
Organism(s): Rattus norvegicus, Mus musculus
Expression System: Pichia
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2017-07-19 Released: 2017-08-30
Deposition Author(s): Pau, V., Zhou, Y., Ramu, Y., Xu, Y., Lu, Z.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.243 (Depositor), 0.246 (DCC)
R-Value Work:
0.236 (Depositor), 0.240 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of an inactivated mutant mammalian voltage-gated K(+) channel.

Pau, V., Zhou, Y., Ramu, Y., Xu, Y., Lu, Z.

(2017) Nat Struct Mol Biol 24: 857-865

PubMed: 28846092 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.3457
Primary Citation Related Structures:
5WIE

PubMed Abstract:
C-type inactivation underlies important roles played by voltage-gated K ⁺ (Kv) channels. Functional studies have provided strong evidence that a common underlying cause of this type of inactivation is an alteration near the extracellular end of the channel's ion-selectivity filter. Unlike N-type inactivation, which is known to reflect occlusion of the channel's intracellular end, the structural mechanism of C-type inactivation remains controversial and may have many detailed variations. Here we report that in voltage-gated Shaker K ⁺ channels lacking N-type inactivation, a mutation enhancing inactivation disrupts the outermost K ⁺ site in the selectivity filter. Furthermore, in a crystal structure of the Kv1.2-2.1 chimeric channel bearing the same mutation, the outermost K ⁺ site, which is formed by eight carbonyl-oxygen atoms, appears to be slightly too small to readily accommodate a K ⁺ ion and in fact exhibits little ion density; this structural finding is consistent with the functional hallmark of C-type inactivation.

Organizational Affiliation

Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Macromolecule Content

Total Structure Weight: 201.91 kDa
Atom Count: 10,955
Modeled Residue Count: 1,370
Deposited Residue Count: 1,730
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-gated potassium channel subunit beta-2	A, C [auth G]	333	Rattus norvegicus	Mutation(s): 0 Gene Names: Kcnab2, Ckbeta2, Kcnb3 EC: 1.1.1 Membrane Entity: Yes
UniProt
Find proteins for P62483 (Rattus norvegicus) Explore P62483 Go to UniProtKB: P62483
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62483
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily A member 2	B, D [auth H]	532	Rattus norvegicus, Mus musculus This entity is chimeric	Mutation(s): 1 Gene Names: Kcna2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63141 (Mus musculus) Explore P63141 Go to UniProtKB: P63141
IMPC: MGI:96659
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63141
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain P [auth H] SDF format, chain H [auth B] SDF format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain P [auth H] MOL2 format, chain H [auth B] MOL2 format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain P [auth H] mmCIF format, chain H [auth B] mmCIF format, chain F [auth B]	F [auth B] G [auth B] H [auth B] I [auth B] J [auth B] F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], P [auth H]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth H] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth H]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth G] MOL2 format, chain E [auth A] MOL2 format, chain O [auth G] mmCIF format, chain E [auth A] mmCIF format, chain O [auth G]	E [auth A], O [auth G]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain O [auth G] Interactions & Density Focus chain E [auth A] Focus chain O [auth G]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Q [auth H] SDF format, chain R [auth H] SDF format, chain T [auth H] SDF format, chain S [auth H] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H] MOL2 format, chain T [auth H] MOL2 format, chain S [auth H] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth H] mmCIF format, chain T [auth H] mmCIF format, chain S [auth H] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	K [auth B] L [auth B] M [auth B] N [auth B] Q [auth H] K [auth B], L [auth B], M [auth B], N [auth B], Q [auth H], R [auth H], S [auth H], T [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.243 (Depositor), 0.246 (DCC)
R-Value Work: 0.236 (Depositor), 0.240 (DCC)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.124	α = 90
b = 143.124	β = 90
c = 284.51	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM055560
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	RO1DK109919

Revision History (Full details and data files)

Version 1.0: 2017-08-30
Type: Initial release
Version 1.1: 2017-09-13
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence
Version 1.3: 2017-10-18
Changes: Database references
Version 1.4: 2019-12-25
Changes: Author supporting evidence
Version 1.5: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description