9KZK: Mouse C3a bound mouse C3aR

Structure of mouse C3a bound mouse C3aR in complex with Go. Determined by electron microscopy at 3.54 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,072
Mol. weight: 170.01 kDa
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9KZK contains 34 α-helices and 61 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	33-40	8	1
α-helix	46-52	7
β-strand	186-192	7	1
β-strand	195-201	7	1
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	1
α-helix	248-255	8
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	284-286	3
α-helix	297-309	13
β-strand	323	1	1
α-helix	331-350	20

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	221-222	2	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-264	6	7
α-helix	272-273	2
β-strand	278	1	8
β-strand	284-287	4	8
β-strand	295-298	4	8
β-strand	303-307	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	68-72	5

Chain E: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-46	26
α-helix	47-51	5
α-helix	58-84	27
α-helix	92-125	34
α-helix	127-133	7
α-helix	136-160	25
β-strand	162-164	3	9
β-strand	171-173	3	9
α-helix	324-334	11
α-helix	335-339	5
α-helix	340-356	17
α-helix	367-395	29
α-helix	401-427	27
α-helix	433-442	10

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	54-55	2

Chain H: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	17-25	9	10
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	68-70	3	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	110-111	2	12
β-strand	115-117	3	12
β-strand	118-119	2	11
β-strand	140-141	2	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	203-208	6	13
β-strand	211-216	6	13
α-helix	221-223	3
β-strand	225-231	7	14
β-strand	239	1	14
β-strand	243-246	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(o) subunit alpha	A	protein	250	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Homo sapiens	P62873 (AlphaFold model)
C3a anaphylatoxin	D	protein	80	Mus musculus	P01027 (AlphaFold model)
Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor	E	protein	533	Homo sapiens, Mus musculus	O09047 (AlphaFold model), P08173
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

Sequence of entity 1 (A), FASTA

>9KZK_1 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYDQVLHEDETTNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPL
TICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIII
ANNLRGCGLY

Sequence of entity 2 (B), FASTA

>9KZK_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>9KZK_3 C3a anaphylatoxin (chains D)
GKSVQLMERRMDKAGQYTDKGLRKCCEDGMRDIPMRYSCQRRARLITQGENCIKAFIDCC
NHITKLREQHRRDHVLGLAR

Sequence of entity 4 (E), FASTA

>9KZK_4 Muscarinic acetylcholine receptor M4,C3a anaphylatoxin chemotactic receptor (chains E)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSESF
DADTNSTDLHSRPLFQPQDIASMVILGLTCLLGLLGNGLVLWVAGVKMKTTVNTVWFLHL
TLADFLCCLSLPFSLAHLILQGHWPYGLFLCKLIPSIIILNMFASVFLLTAISLDRCLIV
HKPIWCQNHRNVRTAFAICGCVWVVAFVMCVPVFVYRDLFIMDNRSICRYNFDSSRSYDY
WDYVYKLSLPESNSTDNSTAQLTGHMNDRSAPSSVQARDYFWTVTTALQSQPFLTSPEDS
FSLDSANQQPHYGGKPPNVLTAAVPSGFPVEDRKSNTLNADAFLSAHTELFPTASSGHLY
PYDFQGDYVDQFTYDNHVPTPLMAITITRLVVGFLVPFFIMVICYSLIVFRMRKTNFTKS
RNKTFRVAVAVVTVFFICWTPYHLVGVLLLITDPESSLGEAVMSWDHMSIALASANSCFN
PFLYALLGKDFRKKARQSIKGILEAAFSEELTHSTNCTQDKASSKRNNMSTDV

Sequence of entity 5 (G), FASTA

>9KZK_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (H), FASTA

>9KZK_6 Antibody fragment - ScFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

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 P09471 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BSB 2.32 Å, Global reconstruction of DRD2 bound to LSD in complex with a mini-GoA and scFv16…
9VJE 2.47 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with buspirone
9K20 2.65 Å, Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGo-scFv16 complex
9VJ5 2.69 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone
8E9X 2.7 Å, CryoEM structure of miniGo-coupled hM4Di in complex with DCZ
9T88 2.74 Å, Cryo-EM structure of ESG-2-37-bound D3 dopamine receptor with mini-Go
9VNF 2.74 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with (S)-pindolol
8YN7 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with immethridine and miniGo
8YN8 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with proxyfan and miniGo
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
7W2Z 2.8 Å, Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
8XXH 2.8 Å, Structure of CXCR2 bound to CXCL2 (CXCR2-CXCL2-Go Full map)

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