9IYA: GPR55-Fab-Nb-ONO-9710531 complex

Cryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex. Determined by electron microscopy at 3.04 Å resolution. Released 1 Jan 2025.

Method: Electron microscopy
Resolution: 3.04 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,219
Mol. weight: 110.63 kDa
Ligands: A1L3E
Released: 1 Jan 2025

Explore 9IYA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IYA contains 34 α-helices and 57 β-strands across 4 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: 21 helices, 0 β-strands

Element	Residues	Length
α-helix	15-48	34
α-helix	49-51	3
α-helix	54-84	31
α-helix	92-124	33
α-helix	128-132	5
α-helix	135-153	19
α-helix	174-177	4
α-helix	182-186	5
α-helix	187-191	5
α-helix	192-211	20
α-helix	223-253	31
α-helix	261-276	16
α-helix	277-279	3
α-helix	280-283	4
α-helix	285-297	13
α-helix	501-517	17
α-helix	522-540	19
α-helix	560-580	21
α-helix	584-596	13
α-helix	597-601	5
α-helix	608-611	4

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14-15	2	2
β-strand	21-28	8	1
β-strand	35-42	8	3
β-strand	48-55	8	3
β-strand	60-63	4	3
β-strand	72-76	5	1
β-strand	81-86	6	1
α-helix	91-93	3
β-strand	95-103	9	3
α-helix	104	1
α-helix	108-111	4
β-strand	121-123	3	3
β-strand	124-125	2	2
β-strand	136-137	2	4
α-helix	139-141	3
β-strand	149-151	3	5
β-strand	154-159	6	4
β-strand	164-168	5	6
α-helix	169-171	3
β-strand	173	1	6
β-strand	178-179	2	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-195	6	4
β-strand	197-199	3	5
α-helix	203-205	3
β-strand	208-214	7	6
β-strand	219-225	7	6

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	7
β-strand	11-14	4	8
β-strand	21-26	6	7
β-strand	34-39	6	8
β-strand	46-49	4	8
α-helix	54-56	3
β-strand	57	1	9
β-strand	59	1	9
β-strand	64-68	5	7
β-strand	71-75	5	7
β-strand	86-91	6	8
α-helix	95-97	3
β-strand	99-100	2	8
β-strand	104-108	5	8
β-strand	113	1	10
α-helix	114-115	2
β-strand	116-120	5	11
α-helix	121-123	3
α-helix	124-129	6
β-strand	131-141	11	11
β-strand	142	1	10
β-strand	146-152	7	12
β-strand	155-156	2	12
β-strand	161-165	5	11
β-strand	175-184	10	11
α-helix	185-189	5
β-strand	193-200	8	12
β-strand	207-212	6	12

Chain N: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	13
β-strand	11-12	2	14
β-strand	19-23	5	13
β-strand	33-38	6	15
β-strand	46-51	6	15
β-strand	58-60	3	15
β-strand	68-71	4	13
β-strand	80-83	4	13
β-strand	92	1	16
β-strand	96-99	4	15
β-strand	110-111	2	15
β-strand	117	1	16
β-strand	118-119	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G-protein coupled receptor 55,Soluble cytochrome b562	A	protein	412	Homo sapiens	P0ABE7 (AlphaFold model), Q9Y2T6 (AlphaFold model)
anti-BRIL Fab Heavy chain	H	protein	246	Homo sapiens
anti-BRIL Fab Light chain	L	protein	215	Homo sapiens
anti-Fab Nanobody	N	protein	123	Homo sapiens

Sequence of entity 1 (A), FASTA

>9IYA_1 G-protein coupled receptor 55,Soluble cytochrome b562 (chains A)
SGDCLFDGVNELMKTLQFAVHIPTFVLGLLLNLLAIHVFSTFLKNRWPDYAATSIYMINL
AVFDLLLVLSLPFKMVLSQVQSPFPSLCTLVECLYFVSMYGSVWTICFISMDRFLAIRYP
LLVSHLRSPRKAFGICCTIWVLVWTGSIPIYSFHGKVEKYMCFHNMSDDTWSAKVFFPLE
VFGFLLPMGIMGFCCSRSIHILLGRRDHTQDWVQQKACIYTIAASLAVFVVSFLPVHLGF
FLQFLVRNSFIVECRAKQSISFFLQLSMCFSNVNCCLDVFIYYFVIKEFRMNIRAHRPSA
DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDF
RHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTL

Sequence of entity 2 (H), FASTA

>9IYA_2 anti-BRIL Fab Heavy chain (chains H)
WSCIILFLVATATGVHSEISEVQLVESGGGLVQPGGSLRLSCAASGFNVRSFSIHWVRQA
PGKGLEWVAYISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWG
YWPGEPWWKAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEP
VTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDK
KVEPKS

Sequence of entity 3 (L), FASTA

>9IYA_3 anti-BRIL Fab Light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (N), FASTA

>9IYA_4 anti-Fab Nanobody (chains N)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS

Ligands and cofactors

ID	Name	Formula	Copies
A1L3E	4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxi…	C26 H27 Br N2 O5	1

Primary citation

Structure basis of ligand recognition and activation of GPR55. Chang, H., Li, X., Shen, L. et al. Cell Res (2025) 35:80-83. DOI 10.1038/s41422-024-01046-8 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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