6M1I: Human PAC1 receptor

CryoEM structure of human PAC1 receptor in complex with PACAP38. Determined by electron microscopy at 3.5 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 8,916
Mol. weight: 157.6 kDa
Released: 11 Mar 2020

Explore 6M1I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M1I contains 41 α-helices and 50 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: 25 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	26-40	15
α-helix	55-56	2
β-strand	58	1	1
β-strand	63	1	1
β-strand	72-76	5	2
α-helix	79-81	3
α-helix	88-111	3
β-strand	113-118	6	2
β-strand	123-126	4	2
α-helix	130-134	5
α-helix	147-169	23
α-helix	171-175	5
α-helix	186-208	23
α-helix	215-218	4
α-helix	225-238	14
α-helix	245-253	9
α-helix	262-285	24
α-helix	306-308	3
α-helix	311-328	18
α-helix	330-335	6
α-helix	347-350	4
α-helix	352-355	4
α-helix	356-358	3
α-helix	359-362	4
α-helix	364-369	6
α-helix	374-377	4
α-helix	381-387	7
α-helix	392-397	6
α-helix	398-402	5
α-helix	408-418	11

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-23	22

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	3
β-strand	10	1	4
β-strand	17-23	7	3
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	45-51	7	4
β-strand	58-60	3	4
α-helix	62-64	3
β-strand	68-73	6	3
β-strand	78-84	7	3
α-helix	88-90	3
β-strand	92-98	7	4
β-strand	118	1	4
β-strand	122-124	3	4

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-21	15
α-helix	30-43	14

Chain E: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	37-39	3
β-strand	47-51	5	5
β-strand	58-62	5	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	88-94	7	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	121-125	5	7
β-strand	135-139	5	7
β-strand	146-151	6	8
β-strand	157-161	5	8
β-strand	166-170	5	8
β-strand	175-180	6	8
β-strand	187-192	6	9
β-strand	199-203	5	9
β-strand	207-211	5	9
β-strand	218-223	6	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	249-254	6	10
β-strand	259-264	6	10
β-strand	275-278	4	11
β-strand	284-288	5	11
β-strand	294-298	5	11
β-strand	304-308	5	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	336-339	4	5

Chain F: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-37	24
β-strand	40-45	6	12
α-helix	50-58	9
β-strand	207-214	8	12
β-strand	217-224	8	12
β-strand	243-246	4	12
α-helix	266-277	12
β-strand	286-290	5	12
α-helix	295-298	4
α-helix	326-327	2
α-helix	332-349	18
β-strand	359-362	4	12
α-helix	371-389	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pituitary adenylate cyclase-activating polypeptide type I receptor	A	protein	406	Homo sapiens	P41586 (AlphaFold model)
Pituitary adenylate cyclase-activating polypeptide	B	protein	38	Homo sapiens	P18509 (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

>6M1I_1 Pituitary adenylate cyclase-activating polypeptide type I receptor (chains A)
DYKDDDDKIFKKEQAMCLEKIQRANELMGFNDSSPGCPGMWDNITCWKPAHVGEMVLVSC
PELFRIFNPDQDMGVVSRNCTEDGWSEPFPHYFDACGFDEYESETGDQDYYYLSVKALYT
VGYSLSLVALLLAMVILCRFRKLHCTRNFIHMNLFVSFMLRAISVFIKDWILYAEQDSNH
CFISTVECKAVMVFFHYCVVSNYFWLFIEGLYLFTLLVETFFPERRYFYWYTIIGWGAPL
VFVTVWATLRLYFDDTGCWDMNDSTALWWVIKGPVVGSIMVNFVLFIGIIVILVQKLQSP
DMGGNESSIYLRLARSTLLLIPLFGIHYTVFAFSPENVSKRERLVFELGLGSFQGFVVAV
LYCFLNGEVQAEIKRKWRSWKVNRYFAVDFKHRHPSLASSLEVLFQ

Sequence of entity 2 (B), FASTA

>6M1I_2 Pituitary adenylate cyclase-activating polypeptide (chains B)
HSDGIFTDSYSRYRKQMAVKKYLAAVLGKRYKQRVKNK

Sequence of entity 3 (C), FASTA

>6M1I_3 Nanobody 35 (chains C)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSHHHHHH

Sequence of entity 4 (D), FASTA

>6M1I_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>6M1I_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

>6M1I_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
6M1H 3.6 Å, CryoEM structure of human PAC1 receptor in complex with maxadilan
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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