8DWG: Proenkephalin-A

CryoEM structure of Gq-coupled MRGPRX1 with peptide ligand BAM8-22 and positive allosteric modulator ML382. Determined by electron microscopy at 2.71 Å resolution. Released 2 Nov 2022.

Method: Electron microscopy
Resolution: 2.71 Å
Organisms: Bos taurus, Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,350
Mol. weight: 139.72 kDa
Ligands: U39
Released: 2 Nov 2022

Explore 8DWG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DWG contains 35 α-helices and 62 β-strands across 5 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 B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-39	7	1
α-helix	46-48	3
β-strand	69	1	2
β-strand	72-76	5	1
β-strand	79-85	7	1
β-strand	86	1	2
α-helix	96-98	3
β-strand	105-111	7	1
α-helix	115-117	3
α-helix	118-129	12
α-helix	132-134	3
β-strand	138-144	7	1
α-helix	146-154	9
α-helix	160-163	4
α-helix	165-167	3
α-helix	184-203	20
β-strand	211-215	5	1
α-helix	223-242	20

Chain C: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	34-36	3
β-strand	43	1	3
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	89-94	6	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	165-170	6	7
β-strand	175-181	7	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	218-222	5	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	3
β-strand	284-289	6	3
β-strand	294-298	5	3
β-strand	303-308	6	3
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	53-55	3

Chain E: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-119	5	11
β-strand	128-129	2	12
β-strand	134-136	3	13
β-strand	143-147	5	14
β-strand	148-149	2	12
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	13
β-strand	174-178	5	13
β-strand	182-183	2	13
α-helix	184	1
β-strand	191-196	6	14
β-strand	199-204	6	14
β-strand	213-219	7	13
α-helix	225	1
β-strand	226	1	13
β-strand	231-234	4	13

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	24-52	29
α-helix	60-87	28
α-helix	93-97	5
α-helix	99-125	27
α-helix	127-128	2
α-helix	129-133	5
α-helix	138-160	23
α-helix	171-203	33
α-helix	212-228	17
α-helix	231-238	8
α-helix	246-248	3
α-helix	249-254	6
α-helix	255-265	11
α-helix	268-272	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proenkephalin-A	A	protein	15	Bos taurus	P01210 (AlphaFold model)
Gs-mini-Gq chimera	B	protein	246	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
Mas-related G-protein coupled receptor member X1	R	protein	323	Homo sapiens	Q96LB2 (AlphaFold model)
scFv16	E	protein	257	Mus musculus

Sequence of entity 1 (A), FASTA

>8DWG_1 Proenkephalin-A (chains A)
VGRPEWWMDYQKRYG

Sequence of entity 2 (B), FASTA

>8DWG_2 Gs-mini-Gq chimera (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 3 (C), FASTA

>8DWG_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>8DWG_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>8DWG_5 Mas-related G-protein coupled receptor member X1 (chains R)
GPDPTISTLDTELTPINGTEETLCYKQTLSLTVLTCIVSLVGLTGNAVVLWLLGCRMRRN
AFSIYILNLAAADFLFLSGRLIYSLLSFISIPHTISKILYPVMMFSYFAGLSFLSAVSTE
RCLSVLWPIWYRCHRPTHLSAVVCVLLWALSLLRSILEWMLCGFLFSGADSAWCQTSDFI
TVAWLIFLCVVLCGSSLVLLIRILCGSRKIPLTRLYVTILLTVLVFLLCGLPFGIQFFLF
LWIHVDREVLFCHVHLVSIFLSALNSSANPIIYFFVGSFRQRQNRQNLKLVLQRALQDAS
EVDEGGGQLPEEILELSGSRLEQ

Sequence of entity 6 (E), FASTA

>8DWG_6 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
U39	2-[(cyclopropanesulfonyl)amino]-N-(2-ethoxyphenyl)benzamide	C18 H20 N2 O4 S	1

Primary citation

Ligand recognition and allosteric modulation of the human MRGPRX1 receptor. Liu, Y., Cao, C., Huang, X.P. et al. Nat Chem Biol (2023) 19:416-422. DOI 10.1038/s41589-022-01173-6 · PubMed

Other PDB entries of the same protein (UniProt P01210 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5E33 1.84 Å, Structure of human DPP3 in complex with met-enkephalin
5E3A 2.05 Å, Structure of human DPP3 in complex with opioid peptide leu-enkephalin
8JGF 2.7 Å, CryoEM structure of Gq-coupled MRGPRX1 with peptide agonist BAM8-22
8DWC 2.87 Å, CryoEM structure of Gq-coupled MRGPRX1 with peptide agonist BAM8-22
8JGG 3.0 Å, CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22
1PLW NMR structure of Methionine-Enkephalin in fast tumbling DMPC/DHPC bicelles
1PLX NMR structure of Methionine-Enkephalin in fast tumbling Bicelles/DMPG
2LWC Met-enkephalin in DPMC SUV

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