9KWX: Mouse C5a-desArg bound mouse C5aR1

Structure of mouse C5a-desArg bound mouse C5aR1 in complex with Go. Determined by electron microscopy at 3.13 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.13 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,686
Mol. weight: 154.61 kDa
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9KWX contains 37 α-helices and 65 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-39	3
α-helix	41-60	20
α-helix	64-67	4
α-helix	71-97	27
α-helix	106-109	4
α-helix	112-139	28
α-helix	150-172	23
β-strand	175-178	4	1
β-strand	187-191	5	1
α-helix	201-206	6
α-helix	207-213	7
α-helix	214-230	17
α-helix	239-268	30
α-helix	276-304	29
α-helix	311-314	4

Chain B: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	10-30	21
β-strand	33-37	5	2
β-strand	40	1	3
α-helix	46-52	7
β-strand	187-192	6	2
β-strand	195-200	6	2
α-helix	202-204	3
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-222	2	2
β-strand	225-227	3	3
α-helix	245-255	11
β-strand	265	1	2
β-strand	268-270	3	3
α-helix	272-279	8
α-helix	284-286	3
α-helix	297-309	13
β-strand	319	1	2
β-strand	322-323	2	3
α-helix	331-351	21

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
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	88-94	7	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	120-125	6	6
β-strand	134-140	7	6
β-strand	146-153	8	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	10
β-strand	284-289	6	10
β-strand	293-298	6	10
β-strand	303-309	7	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	16-24	9
α-helix	48-63	16
β-strand	67-68	2	1

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	54-55	2

Chain H: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	35-39	5	12
β-strand	45-51	7	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	110-111	2	12
β-strand	115-119	5	12
β-strand	140-142	3	13
β-strand	146-148	3	14
β-strand	155-161	7	13
β-strand	166	1	15
β-strand	172	1	15
β-strand	174-179	6	14
β-strand	186-190	5	14
β-strand	194-195	2	14
β-strand	203-207	5	13
β-strand	211-216	6	13
α-helix	221-223	3
β-strand	226-231	6	14
β-strand	239	1	14
β-strand	243-246	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1	A	protein	407	Homo sapiens, Mus musculus	P08173 (AlphaFold model), P30993 (AlphaFold model)
Guanine nucleotide-binding protein G(o) subunit alpha	B	protein	240	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	256	Mus musculus
C5a anaphylatoxin	F	protein	78	Mus musculus	P06684

Sequence of entity 1 (A), FASTA

>9KWX_1 Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1 (chains A)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDPI
DNSSFEINYDHYGTMDPNIPADGIHLPKRQPGDVAALIIYSVVFLVGVPGNALVVWVTAF
EARRAVNAIWFLNLAVADLLSCLALPVLFTTVLNHNYWYFDATACIVLPSLILLNMYASI
LLLATISADRFLLVFKPIWCQKVRGTGLAWMACGVAWVLALLLTIPSFVYREAYKDFYSE
HTVCGINYGGGSFPKEKAVAILRLMVGFVLPLLTLNICYTFLLLRTWSRKATRSTKTLKV
VMAVVICFFIFWLPYQVTGVMIAWLPPSSPTLKRVEKLNSLCVSLAYINCCVNPIIYVMA
GQGFHGRLLRSLPSIIRNALSEDSVGRDSKTFTPSTTDTSTRKSQAV

Sequence of entity 2 (B), FASTA

>9KWX_2 Guanine nucleotide-binding protein G(o) subunit alpha (chains B)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGP
NTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 3 (C), FASTA

>9KWX_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

>9KWX_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (H), FASTA

>9KWX_5 Antibody fragment ScFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 6 (F), FASTA

>9KWX_6 C5a anaphylatoxin (chains F)
GANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECC
TIANKIRKESPHKPVQLG

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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