8SD3: Rat Kv2.1(1-598) wild type in nanodiscs

CryoEM structure of rat Kv2.1(1-598) wild type in nanodiscs. Determined by electron microscopy at 2.95 Å resolution. Released 27 Sept 2023.

Method: Electron microscopy
Resolution: 2.95 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 7,832
Mol. weight: 292.77 kDa
Ligands: POV
Released: 27 Sept 2023

Explore 8SD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SD3 contains 55 α-helices and 0 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B and D: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	173-176	4
α-helix	178-180	3
α-helix	182-204	23
α-helix	225-245	21
α-helix	252-255	4
α-helix	257-264	8
α-helix	267-276	10
α-helix	289-297	9
α-helix	298-309	12
α-helix	311-322	12
α-helix	324-349	26
α-helix	360-371	12
α-helix	384-402	19
α-helix	405-427	23

Chain C: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	173-176	4
α-helix	182-204	23
α-helix	225-245	21
α-helix	252-255	4
α-helix	257-264	8
α-helix	267-276	10
α-helix	289-297	9
α-helix	298-309	12
α-helix	311-322	12
α-helix	324-349	26
α-helix	360-371	12
α-helix	384-402	19
α-helix	405-427	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Potassium voltage-gated channel subfamily B member 1	A, B, C, D	protein	600	Rattus norvegicus	P15387 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8SD3_1 Potassium voltage-gated channel subfamily B member 1 (chains A, B, C, D)
GTMTKHGSRSTSSLPPEPMEIVRSKACSRRVRLNVGGLAHEVLWRTLDRLPRTRLGKLRD
CNTHDSLLQVCDDYSLEDNEYFFDRHPGAFTSILNFYRTGRLHMMEEMCALSFSQELDYW
GIDEIYLESCCQARYHQKKEQMNEELKREAETLREREGEEFDNTCCAEKRKKLWDLLEKP
NSSVAAKILAIISIMFIVLSTIALSLNTLPELQSLDEFGQSTDNPQLAHVEAVCIAWFTM
EYLLRFLSSPKKWKFFKGPLNAIDLLAILPYYVTIFLTESNKSVLQFQNVRRVVQIFRIM
RILRILKLARHSTGLQSLGFTLRRSYNELGLLILFLAMGIMIFSSLVFFAEKDEDDTKFK
SIPASFWWATITMTTVGYGDIYPKTLLGKIVGGLCCIAGVLVIALPIPIIVNNFSEFYKE
QKRQEKAIKRREALERAKRNGSIVSMNMKDAFARSIEMMDIVVEKNGESIAKKDKVQDNH
LSPNKWKWTKRALSETSSSKSFETKEQGSPEKARSSSSPQHLNVQQLEDMYSKMAKTQSQ
PILNTKEMAPQSKPPEELEMSSMPSPVAPLPARTEGVIDMRSMSSIDSFISCATDFPEAT

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	24

Water and common crystallization additives (K) are not listed.

Primary citation

Inactivation of the Kv2.1 channel through electromechanical coupling. Fernandez-Marino, A.I., Tan, X.F., Bae, C. et al. Nature (2023) 622:410-417. DOI 10.1038/s41586-023-06582-8 · PubMed

Other PDB entries of the same protein (UniProt P15387 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JTA 2.5 Å, Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin
4JTD 2.54 Å, Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of…
4JTC 2.56 Å, Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin in Cs+
3LNM 2.9 Å, F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel
8SDA 3.32 Å, CryoEM structure of rat Kv2.1(1-598) L403A mutant in nanodiscs

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