6M1H: Human PAC1 receptor

CryoEM structure of human PAC1 receptor in complex with maxadilan. Determined by electron microscopy at 3.6 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Lutzomyia longipalpis, Lama glama
Chains: 6
Atoms: 9,036
Mol. weight: 160.58 kDa
Released: 11 Mar 2020

Explore 6M1H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M1H contains 37 α-helices and 62 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: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	29-35	7
β-strand	54	1	1
β-strand	57-58	2	2
β-strand	63-64	2	2
β-strand	67	1	1
β-strand	71-76	6	3
α-helix	79-81	3
β-strand	113-119	7	3
β-strand	122-123	2	3
α-helix	130-133	4
α-helix	147-177	31
α-helix	186-204	19
α-helix	213-217	5
α-helix	225-252	28
α-helix	253-255	3
α-helix	262-267	6
α-helix	275-289	15
α-helix	306-335	30
α-helix	350-362	13
α-helix	367-371	5
α-helix	382-390	9
α-helix	392-396	5
α-helix	408-415	8

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-30	25
α-helix	39-41	3
α-helix	45-55	11

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	4
β-strand	10-11	2	5
β-strand	17-21	5	6
β-strand	24-25	2	4
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-50	6	7
β-strand	60	1	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-84	7	6
β-strand	93-98	6	7
β-strand	118	1	7
β-strand	122-123	2	7
β-strand	124-125	2	5

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-12	5
α-helix	14-23	10
α-helix	30-43	14
α-helix	53-55	3

Chain E: 3 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4-22	19
α-helix	23-25	3
α-helix	30-33	4
β-strand	47-51	5	8
β-strand	58-63	6	9
β-strand	69-74	6	9
β-strand	78-83	6	9
β-strand	89-94	6	9
β-strand	100-105	6	10
β-strand	111-116	6	10
β-strand	121-125	5	10
β-strand	134-139	6	10
β-strand	149-151	3	11
β-strand	157-159	3	11
β-strand	161	1	12
β-strand	166	1	13
β-strand	167-168	2	11
β-strand	169-170	2	14
β-strand	175-176	2	14
β-strand	180	1	13
β-strand	187-192	6	12
β-strand	199-203	5	12
β-strand	207-210	4	12
β-strand	222-223	2	12
β-strand	229-234	6	15
β-strand	240-245	6	15
β-strand	250-254	5	15
β-strand	260-264	5	15
β-strand	273-278	6	16
β-strand	284-289	6	16
β-strand	294-298	5	16
β-strand	304-306	3	16
β-strand	315-320	6	8
β-strand	327-331	5	8
β-strand	336-339	4	8

Chain F: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	16-36	21
β-strand	41-47	7	17
β-strand	207	1	18
β-strand	210-214	5	17
β-strand	217-223	7	17
β-strand	224	1	18
β-strand	243-247	5	17
α-helix	265-277	13
β-strand	286-290	5	17
β-strand	291	1	19
α-helix	306-311	6
α-helix	313-317	5
α-helix	318-321	4
α-helix	325-327	3
α-helix	334-349	16
β-strand	359-360	2	17
β-strand	363	1	19
α-helix	373-390	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pituitary adenylate cyclase-activating polypeptide type I receptor	A	protein	410	Homo sapiens	P41586 (AlphaFold model)
Maxadilan	B	protein	61	Lutzomyia longipalpis	P30659 (AlphaFold model)
Nanobody 35	C	protein	134	Lama glama
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	E	protein	341	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	F	protein	394	Homo sapiens	P63092

Sequence of entity 1 (A), FASTA

>6M1H_1 Pituitary adenylate cyclase-activating polypeptide type I receptor (chains A)
DYKDDDDKIFKKEQAMCLEKIQRANELMGFNDSSPGCPGMWDNITCWKPAHVGEMVLVSC
PELFRIFNPDQDMGVVSRNCTEDGWSEPFPHYFDACGFDEYESETGDQDYYYLSVKALYT
VGYSLSLVALLLAMVILCRFRKLHCTRNFIHMNLFVSFMLRAISVFIKDWILYAEQDSNH
CFISTVECKAVMVFFHYCVVSNYFWLFIEGLYLFTLLVETFFPERRYFYWYTIIGWGAPL
VFVTVWATLRLYFDDTGCWDMNDSTALWWVIKGPVVGSIMVNFVLFIGIIVILVQKLQSP
DMGGNESSIYLRLARSTLLLIPLFGIHYTVFAFSPENVSKRERLVFELGLGSFQGFVVAV
LYCFLNGEVQAEIKRKWRSWKVNRYFAVDFKHRHPSLASSHHHHHHHHHH

Sequence of entity 2 (B), FASTA

>6M1H_2 Maxadilan (chains B)
CDATCQFRKAIDDCQKQAHHSNVLQTSVQTTATFTSMDTSQLPGNSVFKECMKQKKKEFK
A

Sequence of entity 3 (C), FASTA

>6M1H_3 Nanobody 35 (chains C)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSHHHHHH

Sequence of entity 4 (D), FASTA

>6M1H_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>6M1H_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains E)
GMSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIY
AMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDN
ICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTT
FTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGN
AFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDA
LKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 6 (F), FASTA

>6M1H_6 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains F)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL

Primary citation

Cryo-EM structures of PAC1 receptor reveal ligand binding mechanism. Wang, J., Song, X., Zhang, D. et al. Cell Res (2020) 30:436-445. DOI 10.1038/s41422-020-0280-2 · PubMed

Other PDB entries of the same protein (UniProt P41586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3N94 1.8 Å, Crystal structure of human pituitary adenylate cyclase 1 Receptor-short N-terminal…
8E3X 2.3 Å, Cryo-EM structure of the PAC1R-PACAP27-Gs complex
7JQD 2.7 Å, Crystal Structure of PAC1r in complex with peptide antagonist
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
9P93 3.2 Å, Cryo-EM structure of the PAC1sR-VIP-Gs complex
6M1I 3.5 Å, CryoEM structure of human PAC1 receptor in complex with PACAP38
9P92 3.8 Å, Cryo-EM structure of the PAC1nR-VIP-Gs complex
6LPB 3.9 Å, Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G…
2JOD Pac1-Rshort N-terminal EC domain Pacap(6-38) complex

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