8IA2: C5a bound human C5aR1

Structure of C5a bound human C5aR1 in complex with Go (Composite map). Determined by electron microscopy at 3.21 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,653
Mol. weight: 154.62 kDa
Released: 18 Oct 2023

Explore 8IA2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IA2 contains 45 α-helices and 75 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: 16 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	37-52	16
α-helix	55-60	6
α-helix	61-65	5
α-helix	70-72	3
α-helix	73-87	15
α-helix	89-97	9
β-strand	101	1	1
α-helix	106-139	34
α-helix	141-147	7
α-helix	150-174	25
β-strand	175-179	5	1
β-strand	186-190	5	1
α-helix	199-207	9
α-helix	208-212	5
α-helix	213-229	17
α-helix	239-267	29
α-helix	272-303	32
α-helix	305-307	3
α-helix	308-313	6

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-30	21
β-strand	34-37	4	2
β-strand	40	1	3
α-helix	46-52	7
β-strand	186	1	4
β-strand	189-191	3	2
β-strand	196-200	5	2
β-strand	201	1	4
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	245-254	10
α-helix	258-260	3
β-strand	264-265	2	2
β-strand	268-270	3	3
α-helix	272-281	10
α-helix	284-286	3
α-helix	297-309	13
β-strand	319	1	2
β-strand	322	1	3
α-helix	330-350	21

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	34-36	3
β-strand	47-51	5	5
β-strand	58-63	6	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	88-94	7	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	121-125	5	7
β-strand	134-139	6	7
β-strand	146-153	8	8
β-strand	156-161	6	8
β-strand	165-170	6	8
β-strand	175-181	7	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	208-212	5	9
β-strand	218-222	5	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	249-254	6	10
β-strand	259-264	6	10
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	294-298	5	11
β-strand	304-307	4	11
β-strand	317-320	4	5
β-strand	327-330	4	5
β-strand	336-339	4	5

Chain D: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-10	9
α-helix	16-25	10
α-helix	34-37	4
α-helix	38-40	3
α-helix	45-65	21
β-strand	68	1	1

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-24	16
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3

Chain H: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	6-7	2	13
β-strand	10-12	3	14
β-strand	17-23	7	13
β-strand	25	1	12
α-helix	29-31	3
β-strand	33-35	3	15
β-strand	38-39	2	14
β-strand	45-46	2	14
β-strand	49-51	3	15
α-helix	53-55	3
β-strand	58-60	3	15
β-strand	65	1	13
β-strand	68-73	6	13
α-helix	74-76	3
β-strand	78-84	7	13
α-helix	88-90	3
β-strand	92-94	3	14
β-strand	97-99	3	15
β-strand	111	1	15
β-strand	115-119	5	14
β-strand	140-141	2	16
β-strand	146-148	3	17
β-strand	155-161	7	16
β-strand	166	1	18
β-strand	172	1	18
β-strand	174-178	5	19
β-strand	179	1	17
β-strand	186-190	5	19
β-strand	194-195	2	19
α-helix	196	1
β-strand	203-208	6	16
β-strand	211-216	6	16
α-helix	221-223	3
β-strand	226	1	17
β-strand	229-231	3	19
β-strand	244-246	3	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C5a anaphylatoxin chemotactic receptor 1	A	protein	406	Homo sapiens	P21730 (AlphaFold model)
C5a anaphylatoxin	D	protein	74	Homo sapiens	P01031 (AlphaFold model)
Guanine nucleotide-binding protein G(o) subunit alpha	B	protein	250	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	248	Mus musculus

Sequence of entity 1 (A), FASTA

>8IA2_1 C5a anaphylatoxin chemotactic receptor 1 (chains A)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDSF
NYTTPDYGHYDDKDTLDLNTPVDKTSNTLRVPDILALVIFAVVFLVGVLGNALVVWVTAF
EAKRTINAIWFLNLAVADFLSCLALPILFTSIVQHHHWPFGGAACSILPSLILLNMYASI
LLLATISADRFLLVFKPIWCQNFRGAGLAWIACAVAWGLALLLTIPSFLYRVVREEYFPP
KVLCGVDYSHDKRRERAVAIVRLVLGFLWPLLTLTICYTFILLRTWSRRATRSTKTLKVV
VAVVASFFIFWLPYQVTGIMMSFLEPSSPTFLLLKKLDSLCVSFAYINCCINPIIYVVAG
QGFQGRLRKSLPSLLRNVLTEESVVRESKSFTRSTVDTMAQKTQAV

Sequence of entity 2 (D), FASTA

>8IA2_2 C5a anaphylatoxin (chains D)
TLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQ
LRANISHKDMQLGR

Sequence of entity 3 (B), FASTA

>8IA2_3 Guanine nucleotide-binding protein G(o) subunit alpha (chains B)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYDQVLHEDETTNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPL
TICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIII
ANNLRGCGLY

Sequence of entity 4 (C), FASTA

>8IA2_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>8IA2_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (H), FASTA

>8IA2_6 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 P21730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6C1R 2.2 Å, Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53…
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
5O9H 2.7 Å, Crystal structure of thermostabilised human C5a anaphylatoxin chemotactic receptor 1…
7Y67 2.8 Å, Cryo-EM structure of C089-bound C5aR1(I116A) mutant in complex with Gi protein
6C1Q 2.9 Å, Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53…
7Y64 2.9 Å, Cryo-EM structure of C5a-bound C5aR1 in complex with Gi protein
7Y66 2.9 Å, Cryo-EM structure of BM213-bound C5aR1 in complex with Gi protein
8HK5 3.0 Å, C5aR1-Gi-C5a protein complex
9KUG 3.07 Å, Structure of EP67 bound to human C5aR1 in complex with Go
9UMR 3.15 Å, Structure of C5a-pep bound human C5aR1 in complex with Go
7Y65 3.2 Å, Cryo-EM structure of C5a peptide-bound C5aR1 in complex with Gi protein
9UMX 3.2 Å, Structure of EP54 bound human C5aR1 in complex with Go

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