8I97: Apo-C3aR-Go complex

Structure of Apo-C3aR-Go complex (Glacios). Determined by electron microscopy at 3.19 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.19 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,130
Mol. weight: 160.86 kDa
Released: 18 Oct 2023

Explore 8I97 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I97 contains 35 α-helices and 62 β-strands across 5 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-40	7	2
α-helix	46-50	5
β-strand	186-192	7	2
β-strand	195-201	7	2
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	2
α-helix	245-255	11
α-helix	258-260	3
β-strand	265-270	6	2
α-helix	272-281	10
α-helix	284-286	3
α-helix	297-309	13
β-strand	319-323	5	2
α-helix	333-351	19

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	38-39	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
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	157-161	5	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187-192	6	7
β-strand	199-203	5	7
β-strand	208-211	4	7
β-strand	220-222	3	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
α-helix	272	1
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-46	26
α-helix	47-51	5
α-helix	56-83	28
α-helix	92-125	34
α-helix	129-132	4
α-helix	136-152	17
α-helix	155-159	5
β-strand	162-163	2	1
β-strand	172-173	2	1
α-helix	334-341	8
α-helix	342-346	5
α-helix	347-362	16
α-helix	374-389	16
α-helix	391-402	12
α-helix	408-431	24
α-helix	432-436	5
α-helix	440-449	10

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	53-55	3

Chain H: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	12	1	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-94	3	13
β-strand	95-98	4	12
β-strand	110-111	2	12
β-strand	115-117	3	13
β-strand	119	1	11
β-strand	140-141	2	14
β-strand	146-148	3	15
β-strand	155-161	7	14
β-strand	166	1	16
β-strand	172	1	16
β-strand	174-179	6	15
β-strand	186-190	5	15
β-strand	194-195	2	15
α-helix	196	1
β-strand	203-208	6	14
β-strand	211-216	6	14
α-helix	221-223	3
β-strand	225-231	7	15
β-strand	239	1	15
β-strand	243-246	4	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C3a anaphylatoxin chemotactic receptor	C	protein	538	Homo sapiens	Q16581 (AlphaFold model)
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)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Antibody fragment - ScFv16	H	protein	248	Mus musculus

Sequence of entity 1 (C), FASTA

>8I97_1 C3a anaphylatoxin chemotactic receptor (chains C)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSASF
SAETNSTDLLSQPWNEPPVILSMVILSLTFLLGLPGNGLVLWVAGLKMQRTVNTIWFLHL
TLADLLCCLSLPFSLAHLALQGQWPYGRFLCKLIPSIIVLNMFASVFLLTAISLDRCLVV
FKPIWCQNHRNVGMACSICGCIWVVAFVMCIPVFVYREIFTTDNHNRCGYKFGLSSSLDY
PDFYGDPLENRSLENIVQPPGEMNDRLDPSSFQTNDHPWTVPTVFQPQTFQRPSADSLPR
GSARLTSQNLYSNVFKPADVVSPKIPSGFPIEDHETSPLDNSDAFLSTHLKLFPSASSNS
FYESELPQGFQDYYNLGQFTDDDQVPTPLVAITITRLVVGFLLPSVIMIACYSFIVFRMQ
RGRFAKSQSKTFRVAVVVVAVFLVCWTPYHIFGVLSLLTDPETPLGKTLMSWDHVCIALA
SANSCFNPFLYALLGKDFRKKARQSIQGILEAAFSEELTRSTHCPSNNVISERNSTTV

Sequence of entity 2 (A), FASTA

>8I97_2 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYDQVLHEDETTNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPL
TICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIII
ANNLRGCGLY

Sequence of entity 3 (B), FASTA

>8I97_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>8I97_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (H), FASTA

>8I97_5 Antibody fragment - ScFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Primary citation

Molecular basis of anaphylatoxin binding, activation, and signaling bias at complement receptors. Yadav, M.K., Maharana, J., Yadav, R. et al. Cell (2023) 186:4956-4973.e21. DOI 10.1016/j.cell.2023.09.020 · PubMed

Other PDB entries of the same protein (UniProt Q16581 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IPV 2.53 Å, Structure of JR14a-C3aR-Gi-scFv16 complex
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
9KVS 2.81 Å, Structure of SB290157 bound to human C3aR in complex with Go (Receptor Ligand Focused map)
8IA8 2.86 Å, Cryo-EM structure of C3aR-Gi-scFv16 bound with E7 peptide
8ZWG 2.87 Å, cryoEM structure of JR14a bound C3aR-Gi complex
8I95 2.88 Å, Structure of EP54-C3aR-Go complex
8HK2 2.9 Å, C3aR-Gi-C3a protein complex
8ZWF 3.0 Å, cryoEM structure of JR14a bound C3aR-BRIL-BAG2 complex
8J6D 3.1 Å, Structure of EP141-C3aR-Go complex
8I9L 3.18 Å, Structure of C3a-C3aR-Go complex (Composite map)
8HK3 3.2 Å, C3aR-Gi-apo protein complex
8I9S 3.26 Å, Structure of Apo-C3aR-Go complex (Titan)

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