8IA8: C3aR-Gi-scFv16

Cryo-EM structure of C3aR-Gi-scFv16 bound with E7 peptide. Determined by electron microscopy at 2.86 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 2.86 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 6
Atoms: 8,810
Mol. weight: 167.5 kDa
Released: 24 May 2023

Explore 8IA8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IA8 contains 44 α-helices and 64 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: 21 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	21-46	26
α-helix	47-51	5
α-helix	56-73	18
α-helix	75-83	9
α-helix	98-113	16
α-helix	118-125	8
α-helix	127-133	7
α-helix	136-152	17
α-helix	155-160	6
β-strand	161	1	1
β-strand	164-166	3	2
β-strand	169-171	3	2
β-strand	174	1	1
α-helix	331-341	11
α-helix	342-346	5
α-helix	347-362	16
α-helix	374-378	5
α-helix	385-389	5
α-helix	391-395	5
α-helix	408-415	8
α-helix	417-426	10
α-helix	427-429	3
α-helix	431	1
α-helix	432-436	5
α-helix	441-453	13

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-21	17
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	89-94	6	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	166-170	5	7
β-strand	175-180	6	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	218-223	6	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	294-298	5	10
β-strand	304-308	5	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain C: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	33-38	6	3
α-helix	46-52	7
β-strand	185	1	3
β-strand	188-191	4	3
β-strand	194-200	7	3
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	3
α-helix	242-254	13
β-strand	263-269	7	3
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-322	4	3
α-helix	331-350	20

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain S: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	17-24	8	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	110-111	2	12
β-strand	115-119	5	12
α-helix	137-139	3
β-strand	140-141	2	13
β-strand	146-148	3	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	186-190	5	14
β-strand	194-195	2	14
α-helix	196	1
β-strand	203-208	6	15
β-strand	211-216	6	15
β-strand	225-231	7	14
α-helix	237	1
β-strand	238-239	2	14
β-strand	243-246	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ala-ser-lys-leu-gly-leu-ala-arg	L	protein	15	Homo sapiens
C3a anaphylatoxin chemotactic receptor	A	protein	482	Homo sapiens	Q16581 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	351	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	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)
scFv16	S	protein	247	Vicugna pacos

Sequence of entity 1 (L), FASTA

>8IA8_1 ALA-SER-LYS-LEU-GLY-LEU-ALA-ARG (chains L)
WWGKKYRASKLGLAR

Sequence of entity 2 (A), FASTA

>8IA8_2 C3a anaphylatoxin chemotactic receptor (chains A)
MASFSAETNSTDLLSQPWNEPPVILSMVILSLTFLLGLPGNGLVLWVAGLKMQRTVNTIW
FLHLTLADLLCCLSLPFSLAHLALQGQWPYGRFLCKLIPSIIVLNMFASVFLLTAISLDR
CLVVFKPIWCQNHRNVGMACSICGCIWVVAFVMCIPVFVYREIFTTDNHNRCGYKFGLSS
SLDYPDFYGDPLENRSLENIVQPPGEMNDRLDPSSFQTNDHPWTVPTVFQPQTFQRPSAD
SLPRGSARLTSQNLYSNVFKPADVVSPKIPSGFPIEDHETSPLDNSDAFLSTHLKLFPSA
SSNSFYESELPQGFQDYYNLGQFTDDDQVPTPLVAITITRLVVGFLLPSVIMIACYSFIV
FRMQRGRFAKSQSKTFRVAVVVVAVFLVCWTPYHIFGVLSLLTDPETPLGKTLMSWDHVC
IALASANSCFNPFLYALLGKDFRKKARQSIQGILEAAFSEELTRSTHCPSNNVISERNST
TV

Sequence of entity 3 (C), FASTA

>8IA8_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>8IA8_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>8IA8_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (S), FASTA

>8IA8_6 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Primary citation

Cryo-EM structure of C3aR-Gi-scFv16 bound with E7 peptide. Liao, Q., Chen, G., Du, Y. et al. To be published.

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)
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)
8I97 3.19 Å, Structure of Apo-C3aR-Go complex (Glacios)
8HK3 3.2 Å, C3aR-Gi-apo protein complex
8I9S 3.26 Å, Structure of Apo-C3aR-Go complex (Titan)

Browse structure collections

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