6LPB: PDB entry 6LPB

Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein. Determined by electron microscopy at 3.9 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Homo sapiens, Rattus norvegicus, unidentified
Chains: 6
Atoms: 8,817
Mol. weight: 141.5 kDa
Released: 11 Mar 2020

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

Secondary structure: helices and β-sheets

6LPB contains 32 α-helices and 56 β-strands across 6 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: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	14-39	26
β-strand	41-47	7	13
α-helix	54-56	3
β-strand	209-214	6	13
β-strand	217-223	7	13
α-helix	236-238	3
β-strand	244-249	6	13
α-helix	253-255	3
α-helix	256-267	12
β-strand	277-282	6	13
α-helix	284-293	10
α-helix	298-300	3
α-helix	316-317	2
α-helix	322-339	18
β-strand	350	1	13
β-strand	353	1	13
α-helix	361-378	18

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	30-32	3
β-strand	47-49	3	5
β-strand	52	1	6
β-strand	58-63	6	7
β-strand	69-74	6	7
β-strand	79-83	5	7
β-strand	88-93	6	7
β-strand	100-105	6	8
β-strand	111-116	6	8
β-strand	121-125	5	8
β-strand	135-139	5	8
β-strand	146-151	6	9
β-strand	156-161	6	9
β-strand	167-170	4	9
β-strand	175-178	4	9
β-strand	187-192	6	10
β-strand	198-203	6	10
β-strand	208-212	5	10
β-strand	218-222	5	10
β-strand	229-234	6	11
β-strand	240-245	6	11
β-strand	250-254	5	11
β-strand	260-264	5	11
α-helix	272-273	2
β-strand	275-276	2	12
β-strand	284-288	5	12
β-strand	294-298	5	12
β-strand	304-308	5	12
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	335	1	6
β-strand	336-339	4	5

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	30-43	14

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-11	2	15
β-strand	17-25	9	14
β-strand	34-39	6	15
β-strand	46-51	6	15
β-strand	58-60	3	15
β-strand	68-73	6	14
β-strand	78-84	7	14
α-helix	88-90	3
β-strand	92-98	7	15
β-strand	118	1	15
β-strand	122-125	4	15

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23

Chain R: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
β-strand	54	1	1
β-strand	57-58	2	2
β-strand	63-64	2	2
β-strand	67	1	1
β-strand	72-76	5	3
α-helix	81-84	4
β-strand	113-117	5	3
β-strand	118	1	4
β-strand	123	1	4
α-helix	130-133	4
α-helix	147-174	28
α-helix	185-210	26
α-helix	224-256	33
α-helix	264-273	10
α-helix	277-289	13
α-helix	303-306	4
α-helix	311-336	26
α-helix	348-355	8
α-helix	359-362	4
α-helix	378-386	9
α-helix	392-399	8
α-helix	406-413	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pituitary adenylate cyclase-activating polypeptide	P	protein	38	Homo sapiens	P18509 (AlphaFold model)
Pituitary adenylate cyclase-activating polypeptide type I receptor	R	protein	403	Homo sapiens	P41586 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	351	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding…	A	protein	249	Homo sapiens	P63092 (AlphaFold model)
nanobody Nb35	N	protein	137	unidentified
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	68	Bos taurus	P63212

Sequence of entity 1 (P), FASTA

>6LPB_1 Pituitary adenylate cyclase-activating polypeptide (chains P)
HSDGIFTDSYSRYRKQMAVKKYLAAVLGKRYKQRVKNK

Sequence of entity 2 (R), FASTA

>6LPB_2 Pituitary adenylate cyclase-activating polypeptide type I receptor (chains R)
MHSDCIFKKEQAMCLEKIQRANELMGFNDSSPGCPGMWDNITCWKPAHVGEMVLVSCPEL
FRIFNPDQVWETETIGESDFGDSNSLDLSDMGVVSRNCTEDGWSEPFPHYFDACGFDEYE
SETGDQDYYYLSVKALYTVGYSTSLVTLTTAMVILCRFRKLHCTRNFIHMNLFVSFMLRA
ISVFIKDWILYAEQDSNHCFISTVECKAVMVFFHYCVVSNYFWLFIEGLYLFTLLVETFF
PERRYFYWYTIIGWGTPTVCVTVWATLRLYFDDTGCWDMNDSTALWWVIKGPVVGSIMVN
FVLFIGIIVILVQKLQSPDMGGNESSIYLRLARSTLLLIPLFGIHYTVFAFSPENVSKRE
RLVFELGLGSFQGFVVAVLYCFLNGEVQAEIKRKWRSENLYFQ

Sequence of entity 3 (B), FASTA

>6LPB_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (A), FASTA

>6LPB_4 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
GNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILH
GGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNR
LQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDAT
PEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCRDIIQR
MHLRQYELL

Sequence of entity 5 (N), FASTA

>6LPB_5 nanobody Nb35 (chains N)
MGQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASI
SYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYR
GQGTQVTVSSLHHHHHH

Sequence of entity 6 (G), FASTA

>6LPB_6 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFS

Primary citation

Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein. Kobayashi, K., Shihoya, W., Nishizawa, T. et al. Nat Struct Mol Biol (2020) 27:274-280. DOI 10.1038/s41594-020-0386-8 · PubMed

Other PDB entries of the same protein (UniProt P18509 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8E3X 2.3 Å, Cryo-EM structure of the PAC1R-PACAP27-Gs complex
8E3Y 2.3 Å, Cryo-EM structure of the VPAC1R-PACAP27-Gs complex
7VQX 2.74 Å, Cryo-EM structure of human vasoactive intestinal polypeptide receptor 2 (VIP2R) in…
27EM 3.0 Å, Cryo_EM structure of PACAP27_PAC1R_Beta_arrestin 1 complex
9P94 3.0 Å, Cryo-EM structure of the PAC1sR-PACAP27-Gs complex
6P9Y 3.01 Å, PAC1 GPCR Receptor complex
6VN7 3.2 Å, Cryo-EM structure of an activated VIP1 receptor-G protein complex
7WBJ 3.42 Å, Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide…
6M1I 3.5 Å, CryoEM structure of human PAC1 receptor in complex with PACAP38
1GEA Receptor-bound conformation of PACAP21
2D2P The solution structure of micelle-bound peptide
2JOD Pac1-Rshort N-terminal EC domain Pacap(6-38) complex

Browse structure collections

About this viewer

MolViewer shows 6LPB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.