9LMP: Antagonist-bounded inactive human GPR4

Cryo-EM structure of antagonist-bounded inactive human GPR4. Determined by electron microscopy at 2.65 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,224
Mol. weight: 101.29 kDa
Ligands: A1L1E
Released: 2 Jul 2025

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

Secondary structure: helices and β-sheets

9LMP contains 39 α-helices and 43 β-strands across 3 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 H: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	13-15	3	2
β-strand	21-28	8	1
α-helix	32-34	3
β-strand	36-42	7	2
β-strand	48-55	8	2
β-strand	60-63	4	2
α-helix	65-67	3
β-strand	71-76	6	1
α-helix	77-79	3
β-strand	81-86	6	1
α-helix	91-93	3
β-strand	95-102	8	2
α-helix	104	1
α-helix	108-111	4
β-strand	116-117	2	2
β-strand	121-125	5	2
α-helix	128-130	3
β-strand	131	1	3
β-strand	134-138	5	4
α-helix	139-141	3
β-strand	149-159	11	4
β-strand	160	1	3
β-strand	165-168	4	5
α-helix	169-171	3
β-strand	173	1	5
β-strand	177-179	3	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-199	10	4
α-helix	200-203	4
β-strand	208-214	7	5
α-helix	215-217	3
β-strand	219-225	7	5

Chain L: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	6
β-strand	11-14	4	7
β-strand	20-26	7	6
β-strand	34-39	6	7
β-strand	46-50	5	7
β-strand	54-55	2	7
α-helix	56	1
β-strand	63-68	6	6
β-strand	71-76	6	6
α-helix	81-83	3
β-strand	86-91	6	7
α-helix	95-97	3
β-strand	99-100	2	7
β-strand	104-108	5	7
α-helix	114-115	2
β-strand	116-120	5	8
α-helix	124-127	4
β-strand	131-141	11	8
β-strand	147-152	6	9
β-strand	155-156	2	9
α-helix	157	1
β-strand	161-165	5	8
α-helix	166-169	4
β-strand	175-184	10	8
α-helix	185-188	4
β-strand	193-199	7	9
β-strand	207-212	6	9

Chain R: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-47	29
α-helix	52-67	16
α-helix	70-79	10
α-helix	87-120	34
α-helix	126-128	3
α-helix	131-148	18
α-helix	151-154	4
α-helix	157-162	6
β-strand	163	1	10
β-strand	170	1	10
α-helix	177-184	8
α-helix	185-191	7
α-helix	192-231	40
α-helix	235-256	22
α-helix	263-288	26
α-helix	293-336	44
α-helix	338-351	14
α-helix	365-374	10
α-helix	375-377	3
α-helix	378-381	4
α-helix	386-389	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of anti-Bril Fab	H	protein	235	Homo sapiens
Light chain of anti-Bril Fab	L	protein	216	Homo sapiens
G-protein coupled receptor 4,Soluble cytochrome b562	R	protein	462	Homo sapiens	P46093 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9LMP_1 Heavy chain of anti-Bril Fab (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (L), FASTA

>9LMP_2 Light chain of anti-Bril Fab (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIF
PPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>9LMP_3 G-protein coupled receptor 4,Soluble cytochrome b562 (chains R)
MGNHTWEGCHVDSRVDHLFPPSLYIFVIGVGLPTNCLALWAAYRQVQQRNELGVYLMNLS
IADLLYICTLPLWVDYFLHHDNWIHGPGSCKLFGFIFYTNIYISIAFLCCISVDRYLAVA
HPLRFARLRRVKTAVAVSSVVWATELGANSAPLFHDELFRDRYNHTFCFEKFPMEGWVAW
MNLYRVFVGFLFPWALMLLSYRGILRAVDKRKADLEDNWETLNDNLKVIEKADNAAQVKD
ALTKMRAAALDAQKATDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ
LKTTRNAYIQKYLEYLDGLERIKRLALSLIAIVLVCFAPYHVLLLSRSAIYLGRPWDCGF
EERVFSAYHSSLAFTSLNCVADPILYCLVNEGARSDVAKALHNLLRFLASDKPQEMANAS
LTLETPLTSKRNSTAKAMTGSWAATPPSQGDQVQLKMLPPAQ

Ligands and cofactors

ID	Name	Formula	Copies
A1L1E	NE52-QQ57	C24 H28 N6 O	1

Primary citation

Proton perception and activation of a proton-sensing GPCR. Chen, L.N., Zhou, H., Xi, K. et al. Mol Cell (2025) 85:1640-1657.e8. DOI 10.1016/j.molcel.2025.02.030 · PubMed

Other PDB entries of the same protein (UniProt P46093 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9JCO 2.36 Å, Cryo-EM structure of the proton-sensing GPCR (GPR4)-Gs protein complex at pH 6.5
8Z9O 2.4 Å, Cryo-EM structure of human GPR4-Gs complex
8Z9P 2.5 Å, Cryo-EM structure of human GPR4-Gi complex
9JCP 2.55 Å, Cryo-EM structure of the proton-sensing GPCR (GPR4)-Gq protein complex at pH 7.4
9JCQ 2.59 Å, Cryo-EM structure of the proton-sensing GPCR (GPR4)-Gs protein complex at pH 7.4
9JFV 2.67 Å, Cryo-EM structure of GPR4 complexed with miniGs/q in pH6.8
9IV6 2.71 Å, Cryo-EM structure of hGPR4-Gs complex in pH7.0
8Z3Q 2.76 Å, Cryo-EM structure of the hGPR4-Gs complex in pH7.6
9BIP 2.8 Å, Human proton sensing receptor GPR4 in complex with miniGs
9LGM 2.84 Å, Cryo-EM structure of GPR4 complexed with Gs in pH8.0
9JFX 2.87 Å, Cryo-EM structure of GPR4 complexed with miniGs/q in pH7.5
8Z3M 2.9 Å, Cryo-EM structure of the hGPR4-Gq complex in pH6.5

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