6PV8: PDB entry 6PV8

Human alpha3beta4 nicotinic acetylcholine receptor in complex with AT-1001. Determined by electron microscopy at 3.87 Å resolution. Released 11 Sept 2019.

Method: Electron microscopy
Resolution: 3.87 Å
Organisms: Homo sapiens, Escherichia coli O11, Mus musculus
Chains: 9
Atoms: 20,051
Mol. weight: 411.78 kDa
Ligands: Y01, P1M, NAG
Released: 11 Sept 2019

Explore 6PV8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PV8 contains 68 α-helices and 135 β-strands across 9 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: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	29-44	16	1
β-strand	49-61	13	1
β-strand	77-81	5	1
β-strand	90	1	2
β-strand	95	1	1
α-helix	101-103	3
β-strand	107-111	5	1
β-strand	115-118	4	1
β-strand	121-126	6	1
β-strand	139-146	8	3
β-strand	148	1	2
β-strand	156-160	5	1
β-strand	164	1	4
β-strand	166	1	1
β-strand	176-180	5	3
β-strand	182	1	4
β-strand	183-189	7	3
β-strand	196-208	13	3
α-helix	214-218	5
α-helix	219-225	7
α-helix	230-233	4
α-helix	241-262	22
α-helix	272-298	27
α-helix	310-313	4
α-helix	314-318	5
α-helix	411-459	49
α-helix	460-465	6

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	11-16	6
β-strand	33	1	5
β-strand	36-48	13	6
β-strand	53-65	13	6
β-strand	81-85	5	6
β-strand	94-96	3	7
β-strand	99	1	6
β-strand	111-115	5	6
β-strand	119-122	4	6
β-strand	125-130	6	6
β-strand	143-152	10	7
β-strand	160	1	5
β-strand	163-164	2	6
β-strand	168	1	8
β-strand	170	1	6
α-helix	174-176	3
β-strand	180-184	5	7
β-strand	186	1	8
β-strand	187-189	3	7
β-strand	201-209	9	7
α-helix	212-214	3
α-helix	215-219	5
α-helix	220-227	8
α-helix	242-263	22
α-helix	273-297	25
α-helix	298-300	3
α-helix	310-314	5
α-helix	315-319	5
α-helix	320-323	4
α-helix	401-456	56

Chain C: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
β-strand	33-38	6	9
β-strand	40	1	10
β-strand	41-48	8	11
β-strand	53-58	6	11
β-strand	61-65	5	9
β-strand	84	1	12
α-helix	86-88	3
β-strand	94-96	3	13
β-strand	99	1	11
β-strand	112	1	12
β-strand	113-114	2	9
β-strand	119-122	4	9
β-strand	126-131	6	11
β-strand	143-152	10	13
β-strand	160-164	5	9
β-strand	168	1	14
β-strand	170	1	10
β-strand	180-184	5	13
β-strand	186	1	14
β-strand	187-189	3	13
β-strand	201-209	9	13
α-helix	212-218	7
α-helix	220-224	5
α-helix	242-263	22
α-helix	273-297	25
α-helix	298-300	3
α-helix	310-315	6
α-helix	320-323	4
α-helix	401-456	56

Chain D: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	27-28	2
β-strand	29-44	16	15
β-strand	49-60	12	15
α-helix	69-71	3
β-strand	78	1	15
β-strand	81	1	16
β-strand	90	1	17
β-strand	95	1	15
α-helix	101-103	3
β-strand	107	1	16
β-strand	108-110	3	15
β-strand	116-118	3	15
β-strand	121-126	6	15
β-strand	139-147	9	18
β-strand	148	1	17
β-strand	156-160	5	15
β-strand	164	1	19
β-strand	166	1	15
α-helix	170-172	3
β-strand	176-180	5	18
β-strand	182	1	19
β-strand	183-189	7	18
β-strand	196-208	13	18
α-helix	214-218	5
α-helix	219-224	6
α-helix	225-227	3
α-helix	231-233	3
α-helix	241-262	22
α-helix	272-298	27
α-helix	310-313	4
α-helix	314-318	5
α-helix	319-322	4
α-helix	411-460	50
α-helix	461-465	5
α-helix	466-468	3

Chain E: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
β-strand	33-48	16	20
β-strand	53-65	13	20
β-strand	82-84	3	20
α-helix	86-88	3
β-strand	94-96	3	21
β-strand	99	1	20
β-strand	112-114	3	20
β-strand	119-122	4	20
β-strand	126-131	6	20
β-strand	143-152	10	21
β-strand	160-164	5	20
β-strand	168	1	22
β-strand	170	1	20
α-helix	174-176	3
β-strand	180-184	5	21
β-strand	186	1	22
β-strand	187-191	5	21
β-strand	199-209	11	21
α-helix	212-214	3
α-helix	215-219	5
α-helix	220-229	10
α-helix	242-263	22
α-helix	273-297	25
α-helix	310-314	5
α-helix	315-319	5
α-helix	320-323	4
α-helix	401-456	56

Chain F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	23
β-strand	29-30	2	24
β-strand	37-44	8	23
β-strand	51-58	8	24
β-strand	64-70	7	24
β-strand	77-79	3	24
β-strand	88-90	3	23
β-strand	97-102	6	23
α-helix	107-109	3
β-strand	111-119	9	24
β-strand	128-129	2	24
β-strand	133-136	4	24

Chain G: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	25
β-strand	32-34	3	26
β-strand	41-46	6	25
β-strand	55-59	5	26
β-strand	66-70	5	26
β-strand	74-75	2	26
β-strand	83-88	6	25
β-strand	91-96	6	25
β-strand	105-110	6	26
β-strand	111	1	27
β-strand	118	1	27
β-strand	123-126	4	26

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	28
β-strand	29-30	2	29
β-strand	37-44	8	28
β-strand	51-58	8	29
β-strand	65-70	6	29
β-strand	78-79	2	29
α-helix	81-83	3
β-strand	87-90	4	28
β-strand	97-102	6	28
α-helix	107-109	3
β-strand	111-119	9	29
β-strand	128-129	2	29
β-strand	133-136	4	29

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fusion protein of Neuronal acetylcholine receptor subunit alpha-3 and Soluble cytochrome b562	A, D	protein	525	Homo sapiens, Escherichia coli O11	P32297 (AlphaFold model)
Fusion protein of Neuronal acetylcholine receptor subunit beta-4 and Soluble cytochrome b562	B, C, E	protein	538	Homo sapiens, Escherichia coli O11	P30926 (AlphaFold model)
IgG2b Fab heavy chain	F, H	protein	219	Mus musculus
Kappa Fab light chain	G, I	protein	213	Mus musculus

Sequence of entity 1 (A, D), FASTA

>6PV8_1 Fusion protein of Neuronal acetylcholine receptor subunit alpha-3 and Soluble cytochrome b562 (chains A, D)
SEAEHRLFERLFEDYNEIIRPVANVSDPVIIHFEVSMSQLVKVDEVNQIMETNLWLKQIW
NDYKLKWNPSDYGGAEFMRVPAQKIWKPDIVLYNNAVGDFQVDDKTKALLKYTGEVTWIP
PAIFKSSCKIDVTYFPFDYQNCTMKFGSWSYDKAKIDLVLIGSSMNLKDYWESGEWAIIK
APGYKHDIKYNCCEEIYPDITYSLYIRRLPLFYTINLIIPCLLISFLTVLVFYLPSDCGE
KVTLCISVLLSLTVFLLVITETIPSTSLVIPLIGEYLLFTMIFVTLSIVITVFVLNVHYR
TPTTHTMPSWVKTVFLNLLPRVMFMTRPTSNEGNAQKPRPLYGAELSADLEDNWETLNDN
LKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQID
DALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLLSALSPEIKEAIQSVKYIAENMKAQNE
AKEIQDDWKYVAMVIDRIFLWVFTLVCILGTAGLFLQPLMAREDA

Sequence of entity 2 (B, C, E), FASTA

>6PV8_2 Fusion protein of Neuronal acetylcholine receptor subunit beta-4 and Soluble cytochrome b562 (chains B, C, E)
RVANAEEKLMDDLLNKTRYNNLIRPATSSSQLISIKLQLSLAQLISVNEREQIMTTNVWL
KQEWTDYRLTWNSSRYEGVNILRIPAKRIWLPDIVLYNNADGTYEVSVYTNLIVRSNGSV
LWLPPAIYKSACKIEVKYFPFDQQNCTLKFRSWTYDHTEIDMVLMTPTASMDDFTPSGEW
DIVALPGRRTVNPQDPSYVDVTYDFIIKRKPLFYTINLIIPCVLTTLLAILVFYLPSDCG
EKMTLCISVLLALTFFLLLISKIVPPTSLDVPLIGKYLMFTMVLVTFSIVTSVCVLNVHH
RSPSTHTMAPWVKRCFLHKLPTFLFMKRPGPDSSPARAFPADLEDNWETLNDNLKVIEKA
DNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLAN
EGKVKEAQAAAEQLKTTRNAYIQKYLSGRFRQDVQEALEGVSFIAQHMKNDDEDQSVVED
WKYVAMVVDRLFLWVFMFVCVLGTVGLFLPPLFQTHAASEGPYAAQRDSAWSHPQFEK

Sequence of entity 3 (F, H), FASTA

>6PV8_3 IgG2b Fab heavy chain (chains F, H)
QVQLQQSGPELVRPGVSVKISCKGSGYTFTDYALYWVRQSHAKSLEWIGVINPYSGNTNY
NQKFKGKATMTVDKSSSTAYMELARLTSDDSAIYYCASGYDGYPYTMDYWGPGASVTVSS
AKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSG
LYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP

Sequence of entity 4 (G, I), FASTA

>6PV8_4 Kappa Fab light chain (chains G, I)
QIVLTQSPAIMSASPGEKVTMTCSASSSMTYMHWYQQKSGTSPKRWIYDTSQLASGVPAR
FRGSGSGTSFSLTISSMEAEDAATYYCQQWSSNPLTFGGGTKLELKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	10
P1M	(3-endo)-N-(2-bromophenyl)-9-methyl-9-azabicyclo[3.3.1]nonan-3-amine	C15 H21 Br N2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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

Primary citation

Agonist Selectivity and Ion Permeation in the alpha 3 beta 4 Ganglionic Nicotinic Receptor. Gharpure, A., Teng, J., Zhuang, Y. et al. Neuron (2019) 104:501. DOI 10.1016/j.neuron.2019.07.030 · PubMed

Other PDB entries of the same protein (UniProt P32297 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ZK4 1.9 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
5TVC 1.93 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
5SYO 2.0 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica…
6PV7 3.34 Å, Human alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine

Browse structure collections

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