6EBM: PDB entry 6EBM

The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs, transmembrane domain of subunit alpha. Determined by electron microscopy at 4.0 Å resolution. Released 22 Aug 2018.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 8,532
Mol. weight: 235.62 kDa
Released: 22 Aug 2018

Explore 6EBM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EBM contains 63 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 B, D and H: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	121-130	10
α-helix	146-152	7
α-helix	160-183	24
α-helix	204-205	2
α-helix	206-210	5
α-helix	221-242	22
α-helix	248-251	4
α-helix	254-275	22
α-helix	287-295	9
α-helix	296-305	10
α-helix	308-318	11
α-helix	324-345	22
α-helix	360-368	9
α-helix	381-398	18
α-helix	402-413	12
α-helix	414-416	3

Chain F: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	121-130	10
α-helix	146-152	7
α-helix	160-183	24
α-helix	204-209	6
α-helix	221-242	22
α-helix	248-251	4
α-helix	254-274	21
α-helix	287-295	9
α-helix	296-305	10
α-helix	308-318	11
α-helix	323-345	23
α-helix	360-368	9
α-helix	381-398	18
α-helix	402-413	12
α-helix	414-416	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily B…	B, D, F, H	protein	513	Rattus norvegicus	P63142 (AlphaFold model), Q63099 (AlphaFold model)

Sequence of entity 1 (B, D, F, H), FASTA

>6EBM_1 Potassium voltage-gated channel subfamily A member 2,Potassium voltage-gated channel subfamily B member 2 chimera (chains B, D, F, H)
MAHHHHHHHHENLYFQGSMTVATGDPVDEAAAHPGHPQDTYDPEADHECCERVVINISGL
RFETQLKTLAQFPETLLGDPKKRMRYFDPLRNEYFFDRNRPSFDAILYYYQSGGRLRRPV
NVPLDIFSEEIRFYELGEEAMEMFREDEGYIKEEERPLPENEFQRQVWLLFEYPESSGPA
RIIAIVSVMVILISIVSFCLETLPIFRDENEDMHGGGVTFHTYSQSTIGYQQSTSFTDPF
FIVETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQF
QNVRRVVQIFRIMRILRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAV
YFAEADERDSQFPSIPDAFWWAVVSMTTVGYGDMVPTTIGGKIVGSLCAIAGVLTIALPV
PVIVSNFNYFYHRETEGEEQAQYLQVTSCPKIPSSPDLKKSRSASTISKSDYMEIQEGVN
NSNEDFREENLKTANCTLANTNYVNITKMLTDV

Primary citation

Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs. Matthies, D., Bae, C., Toombes, G.E. et al. Elife (2018) 7. DOI 10.7554/eLife.37558 · PubMed

Other PDB entries of the same protein (UniProt P63142 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DSX 1.6 Å, KV1.2 T1 domain, residues 33-119, T46V mutant
1QDV 1.6 Å, N-terminal domain, voltage-gated potassium channel KV1.2 residues 33-131
1QDW 2.1 Å, N-terminal domain, voltage-gated potassium channel KV1.2 residues 33-119
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…
8VCH 2.55 Å, Voltage gated potassium ion channel Kv1.2 W366F, C-type inactivated
4JTC 2.56 Å, Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin in Cs+
2A79 2.9 Å, Mammalian Shaker Kv1.2 potassium channel- beta subunit complex
3LNM 2.9 Å, F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel
3LUT 2.9 Å, A Structural Model for the Full-length Shaker Potassium Channel Kv1.2
6EBL 3.0 Å, The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs, cytosolic…
7SIZ 3.1 Å, C-type inactivation in a voltage gated K+ channel

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