8I9L: C3a-C3aR-Go complex

Structure of C3a-C3aR-Go complex (Composite map). Determined by electron microscopy at 3.18 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.18 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,617
Mol. weight: 169.98 kDa
Released: 18 Oct 2023

Explore 8I9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I9L contains 34 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	33-40	8	9
α-helix	46-52	7
β-strand	186-192	7	9
β-strand	195-201	7	9
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	9
α-helix	245-255	11
β-strand	265-270	6	9
α-helix	272-281	10
α-helix	297-309	13
β-strand	320-323	4	9
α-helix	331-350	20

Chain B: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	30-32	3
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	89-94	6	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	120-125	6	3
β-strand	134-140	7	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	178-181	4	4
β-strand	187	1	5
β-strand	191-192	2	6
β-strand	198-202	5	6
β-strand	203	1	5
β-strand	208-212	5	6
β-strand	220-222	3	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
α-helix	272	1
β-strand	273-275	3	8
β-strand	278	1	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 13 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	136-158	23
β-strand	162-163	2	17
β-strand	172-173	2	17
α-helix	332-341	10
α-helix	342-346	5
α-helix	347-362	16
α-helix	375-389	15
α-helix	391-402	12
α-helix	408-435	28
α-helix	440-449	10

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	4-12	9
α-helix	46-48	3
α-helix	50-70	21

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
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	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	68-73	6	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	146-149	4	14
β-strand	155-159	5	15
β-strand	160-161	2	13
β-strand	166	1	16
β-strand	172	1	16
β-strand	174-179	6	14
β-strand	185-190	6	14
β-strand	194-195	2	14
β-strand	203-208	6	15
β-strand	211-216	6	15
α-helix	221-223	3
β-strand	226-231	6	14
β-strand	239	1	14
β-strand	243-247	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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(o) subunit alpha	A	protein	250	Homo sapiens	P09471 (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
C3a anaphylatoxin chemotactic receptor	C	protein	538	Homo sapiens	Q16581 (AlphaFold model)
C3a anaphylatoxin	D	protein	77	Homo sapiens	P01024

Sequence of entity 1 (B), FASTA

>8I9L_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (A), FASTA

>8I9L_2 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYDQVLHEDETTNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPL
TICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIII
ANNLRGCGLY

Sequence of entity 3 (G), FASTA

>8I9L_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (H), FASTA

>8I9L_4 Antibody fragment - ScFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 5 (C), FASTA

>8I9L_5 C3a anaphylatoxin chemotactic receptor (chains C)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSASF
SAETNSTDLLSQPWNEPPVILSMVILSLTFLLGLPGNGLVLWVAGLKMQRTVNTIWFLHL
TLADLLCCLSLPFSLAHLALQGQWPYGRFLCKLIPSIIVLNMFASVFLLTAISLDRCLVV
FKPIWCQNHRNVGMACSICGCIWVVAFVMCIPVFVYREIFTTDNHNRCGYKFGLSSSLDY
PDFYGDPLENRSLENIVQPPGEMNDRLDPSSFQTNDHPWTVPTVFQPQTFQRPSADSLPR
GSARLTSQNLYSNVFKPADVVSPKIPSGFPIEDHETSPLDNSDAFLSTHLKLFPSASSNS
FYESELPQGFQDYYNLGQFTDDDQVPTPLVAITITRLVVGFLLPSVIMIACYSFIVFRMQ
RGRFAKSQSKTFRVAVVVVAVFLVCWTPYHIFGVLSLLTDPETPLGKTLMSWDHVCIALA
SANSCFNPFLYALLGKDFRKKARQSIQGILEAAFSEELTRSTHCPSNNVISERNSTTV

Sequence of entity 6 (D), FASTA

>8I9L_6 C3a anaphylatoxin (chains D)
SVQLTEKRMDKVGKYPKELRKCCEDGMRENPMRFSCQRRTRFISLGEACKKVFLDCCNYI
TELRRQHARASHLGLAR

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 P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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