6EBK: Voltage-gated potassium channel subunit beta-2

The voltage-activated Kv1.2-2.1 paddle chimera channel in lipid nanodiscs. Determined by electron microscopy at 3.3 Å resolution. Released 22 Aug 2018.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 22,212
Mol. weight: 387.95 kDa
Ligands: NAP
Released: 22 Aug 2018

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

Secondary structure: helices and β-sheets

6EBK contains 155 α-helices and 76 β-strands across 8 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.

Chain A: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	1
β-strand	48-50	3	1
β-strand	52-55	4	2
α-helix	59-63	5
α-helix	66-77	12
β-strand	83-85	3	2
α-helix	90-93	4
α-helix	94-106	13
α-helix	110-112	3
β-strand	114-119	6	2
β-strand	121	1	3
α-helix	126-128	3
β-strand	129	1	3
α-helix	133-146	14
β-strand	152-157	6	2
α-helix	166-178	13
β-strand	182-188	7	2
α-helix	192-204	13
β-strand	212-214	3	2
β-strand	216	1	2
β-strand	218	1	4
β-strand	221	1	4
α-helix	223	1
α-helix	224-228	5
α-helix	229-235	7
β-strand	240-243	4	2
α-helix	254-257	4
α-helix	264-266	3
α-helix	271-278	8
α-helix	280-298	19
α-helix	303-309	7
β-strand	317-322	6	2
α-helix	327-334	8
α-helix	345-355	11

Chains B, D and H: 20 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	34-39	6	5
β-strand	42-47	6	5
α-helix	48-51	4
α-helix	65-68	4
β-strand	69-70	2	5
β-strand	75-78	4	5
α-helix	85-94	10
α-helix	106-113	8
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

Chains C and E: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	6
β-strand	48-50	3	6
β-strand	52-55	4	7
α-helix	59-63	5
α-helix	66-77	12
β-strand	83-85	3	7
α-helix	90-93	4
α-helix	94-106	13
α-helix	110-112	3
β-strand	114-118	5	7
β-strand	121	1	8
α-helix	126-128	3
β-strand	129	1	8
α-helix	133-146	14
β-strand	152-157	6	7
α-helix	166-178	13
β-strand	182-188	7	7
α-helix	192-204	13
β-strand	212-214	3	7
β-strand	216	1	7
β-strand	218	1	9
β-strand	221	1	9
α-helix	223	1
α-helix	224-228	5
α-helix	229-235	7
β-strand	240-243	4	7
α-helix	254-257	4
α-helix	264-266	3
α-helix	271-278	8
α-helix	280-298	19
α-helix	303-309	7
β-strand	317-322	6	7
α-helix	327-334	8
α-helix	345-355	11

Chain F: 19 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	34-39	6	15
β-strand	42-47	6	15
α-helix	48-51	4
α-helix	65-68	4
β-strand	69-70	2	15
β-strand	75-78	4	15
α-helix	85-94	10
α-helix	106-113	8
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

Chain G: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	16
β-strand	48-50	3	16
β-strand	52-55	4	17
α-helix	59-63	5
α-helix	66-77	12
β-strand	83-85	3	17
α-helix	90-93	4
α-helix	94-105	12
α-helix	110-112	3
β-strand	114-118	5	17
β-strand	121	1	18
α-helix	126-128	3
β-strand	129	1	18
α-helix	133-146	14
β-strand	152-157	6	17
α-helix	166-178	13
β-strand	182-188	7	17
α-helix	192-204	13
β-strand	212-214	3	17
β-strand	216	1	17
β-strand	218	1	19
β-strand	221	1	19
α-helix	223	1
α-helix	224-228	5
α-helix	229-235	7
β-strand	240-243	4	17
α-helix	254-257	4
α-helix	264-266	3
α-helix	271-278	8
α-helix	280-298	19
α-helix	303-309	7
β-strand	317-322	6	17
α-helix	327-334	8
α-helix	345-355	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Voltage-gated potassium channel subunit beta-2	A, C, E, G	protein	333	Rattus norvegicus	P62483 (AlphaFold model)
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 (A, C, E, G), FASTA

>6EBK_1 Voltage-gated potassium channel subunit beta-2 (chains A, C, E, G)
MVQFYRNLGKSGLRVSCLGLGTWVTFGGQITDEMAEHLMTLAYDNGINLFDTAEVYAAGK
AEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHIIEGLKASLERLQLEYVDV
VFANRPDPNTPMEETVRAMTHVINQGMAMYWGTSRWSSMEIMEAYSVARQFNLIPPICEQ
AEYHMFQREKVEVQLPELFHKIGVGAMTWSPLACGIVSGKYDSGIPPYSRASLKGYQWLK
DKILSEEGRRQQAKLKELQAIAERLGCTLPQLAIAWCLRNEGVSSVLLGASNAEQLMENI
GAIQVLPKLSSSIVHEIDSILGNKPYSKKDYRS

Sequence of entity 2 (B, D, F, H), FASTA

>6EBK_2 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

Ligands and cofactors

ID	Name	Formula	Copies
NAP	NADP nicotinamide-adenine-dinucleotide phosphate	C21 H28 N7 O17 P3	4

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 P62483 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EAU 1.82 Å, Voltage-dependent K+ channel beta subunit in complex with cortisone
3EB3 2.0 Å, Voltage-dependent K+ channel beta subunit (W121A) in complex with cortisone
3EB4 2.0 Å, Voltage-dependent K+ channel beta subunit (I211R) in complex with cortisone
1EXB 2.1 Å, Structure of the cytoplasmic beta subunit-T1 assembly of voltage-dependent K channels
2R9R 2.4 Å, Shaker family voltage dependent potassium channel (kv1.2-kv2.1 paddle chimera channel)…
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+
1QRQ 2.8 Å, Structure of a voltage-dependent K+ channel beta subunit
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

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