9UMX: EP54 bound human C5aR1

Structure of EP54 bound human C5aR1 in complex with Go. Determined by electron microscopy at 3.2 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,217
Mol. weight: 147.54 kDa
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9UMX contains 32 α-helices and 64 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-52	18
α-helix	55-63	9
α-helix	70-72	3
α-helix	73-86	14
α-helix	89-97	9
α-helix	106-109	4
α-helix	112-139	28
α-helix	141-146	6
α-helix	153-173	21
β-strand	175-178	4	1
β-strand	187-190	4	1
α-helix	200-207	8
α-helix	208-212	5
α-helix	213-229	17
α-helix	240-254	15
α-helix	256-266	11
α-helix	273-302	30
α-helix	310-313	4

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-29	20
β-strand	33-37	5	2
β-strand	40	1	2
α-helix	46-52	7
β-strand	186-191	6	2
β-strand	196-201	6	2
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-222	2	2
β-strand	225-227	3	2
α-helix	245-255	11
β-strand	264-270	7	2
α-helix	272-281	10
α-helix	297-309	13
β-strand	319-323	5	2
α-helix	331-350	20

Chain C: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-32	3
α-helix	34-36	3
β-strand	47-51	5	3
β-strand	60-63	4	4
β-strand	69-73	5	4
β-strand	78-83	6	4
β-strand	88-94	7	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	241-245	5	8
β-strand	249-252	4	8
β-strand	262-264	3	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-307	4	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4-5	2	1

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	30-43	14

Chain H: 2 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	1	12
β-strand	34-39	6	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
β-strand	92-94	3	11
β-strand	99	1	12
β-strand	115-119	5	11
β-strand	141-142	2	13
β-strand	147-148	2	14
β-strand	155-160	6	13
β-strand	166	1	15
β-strand	172	1	15
β-strand	174-179	6	16
β-strand	186-190	5	16
β-strand	194-195	2	16
α-helix	196	1
β-strand	203-208	6	13
β-strand	211-216	6	13
β-strand	226-231	6	16
β-strand	243-244	2	16
β-strand	245-246	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1	A	protein	406	Homo sapiens	P08173 (AlphaFold model), P21730 (AlphaFold model)
Guanine nucleotide-binding protein G(o) subunit alpha	B	protein	250	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	350	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768
Antibody fragment - ScFv16	H	protein	248	Mus musculus
EP54 ligand	D	protein	10	Homo sapiens

Sequence of entity 1 (A), FASTA

>9UMX_1 Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1 (chains A)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDSF
NYTTPDYGHYDDKDTLDLNTPVDKTSNTLRVPDILALVIFAVVFLVGVLGNALVVWVTAF
EAKRTINAIWFLNLAVADFLSCLALPILFTSIVQHHHWPFGGAACSILPSLILLNMYASI
LLLATISADRFLLVFKPIWCQNFRGAGLAWIACAVAWGLALLLTIPSFLYRVVREEYFPP
KVLCGVDYSHDKRRERAVAIVRLVLGFLWPLLTLTICYTFILLRTWSRRATRSTKTLKVV
VAVVASFFIFWLPYQVTGIMMSFLEPSSPTFLLLKKLDSLCVSFAYINCCINPIIYVVAG
QGFQGRLRKSLPSLLRNVLTEESVVRESKSFTRSTVDTMAQKTQAV

Sequence of entity 2 (B), FASTA

>9UMX_2 Guanine nucleotide-binding protein G(o) subunit alpha (chains B)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYDQVLHEDETTNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPL
TICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIII
ANNLRGCGLY

Sequence of entity 3 (C), FASTA

>9UMX_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>9UMX_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (H), FASTA

>9UMX_5 Antibody fragment - ScFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 6 (D), FASTA

>9UMX_6 EP54 ligand (chains D)
YSFKPMPLAR

Primary citation

Molecular fingerprints of a convergent mechanism orchestrating diverse ligand recognition and species-specific pharmacology at the complement anaphylatoxin receptors. Mishra, S., Yadav, M.K., Dalal, A. et al. bioRxiv (2025). DOI 10.1101/2025.05.26.656101 · PubMed

Other PDB entries of the same protein (UniProt P08173 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TRP 2.4 Å, Human M4 muscarinic acetylcholine receptor complex with Gi1 and the agonist iperoxo and…
8FX5 2.45 Å, Human M4 muscarinic acetylcholine receptor complex with Gi1 and xanomeline
7TRQ 2.5 Å, Human M4 muscarinic acetylcholine receptor complex with Gi1 and the agonist iperoxo and…
9N09 2.57 Å, Human M4 muscarinic acetylcholine receptor Gi1 complex (mini-Gsi chimera) bound to the…
5DSG 2.6 Å, Structure of the M4 muscarinic acetylcholine receptor (M4-mT4L) bound to tiotropium
9N29 2.6 Å, hM4Di(GRANPA) in complex with mGsI and diphenhydramine
8E9X 2.7 Å, CryoEM structure of miniGo-coupled hM4Di in complex with DCZ
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
7TRK 2.8 Å, Human M4 muscarinic acetylcholine receptor complex with Gi1 and the agonist iperoxo
7TRS 2.8 Å, Human M4 muscarinic acetylcholine receptor complex with Gi1 and the endogenous agonist…
9KVS 2.81 Å, Structure of SB290157 bound to human C3aR in complex with Go (Receptor Ligand Focused map)
9KV6 2.88 Å, Structure of mouse TLQP21 bound to mouse C3aR in complex with Go

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