7Y65: C5a peptide-bound C5aR1

Cryo-EM structure of C5a peptide-bound C5aR1 in complex with Gi protein. Determined by electron microscopy at 3.2 Å resolution. Released 1 Mar 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, synthetic construct, Mus musculus
Chains: 6
Atoms: 8,721
Mol. weight: 155.47 kDa
Released: 1 Mar 2023

Explore 7Y65 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y65 contains 33 α-helices and 60 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-27	18
β-strand	34-39	6	1
α-helix	46-53	8
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-324	6	1
α-helix	331-350	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	30-33	4
α-helix	38-41	4
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	102-105	4	5
β-strand	111-115	5	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	176-181	6	6
α-helix	186	1
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	262-264	3	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-308	6	9
β-strand	318-320	3	3
β-strand	327-330	4	3
β-strand	336-339	4	3

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-22	16
α-helix	30-44	15
α-helix	45-47	3

Chain D: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-64	30
α-helix	70-87	18
α-helix	89-97	9
α-helix	105-138	34
α-helix	143-146	4
α-helix	150-173	24
β-strand	175-180	6	17
β-strand	185-190	6	17
α-helix	196-207	12
α-helix	208-212	5
α-helix	213-229	17
α-helix	239-267	29
α-helix	273-302	30
α-helix	307-313	7

Chain S: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
β-strand	23-25	3	10
α-helix	29-31	3
β-strand	33-36	4	11
β-strand	49-51	3	11
α-helix	53-55	3
β-strand	58-60	3	11
β-strand	65	1	12
β-strand	68	1	12
β-strand	69-73	5	13
β-strand	78-82	5	13
β-strand	96-99	4	11
α-helix	137-140	4
β-strand	141	1	14
β-strand	155-160	6	14
β-strand	166	1	15
β-strand	172	1	15
β-strand	174-179	6	16
β-strand	185-190	6	16
β-strand	194-195	2	16
β-strand	203-208	6	14
β-strand	211-216	6	14
β-strand	226-231	6	16
α-helix	237	1
β-strand	239	1	16
α-helix	240-242	3
β-strand	243-244	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	356	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
C5apep peptide	L	protein	6	synthetic construct
scFV16	S	protein	267	Mus musculus
C5a anaphylatoxin chemotactic receptor 1	D	protein	339	Homo sapiens	P21730 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7Y65_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>7Y65_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQ
MRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCA
YAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDT
TCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTG
HESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRL
LLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>7Y65_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (L), FASTA

>7Y65_4 C5apep peptide (chains L)
FKPAAR

Sequence of entity 5 (S), FASTA

>7Y65_5 scFV16 (chains S)
MDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIY
YADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTV
SSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLELKAAAENLYFQGHHHHHHHH

Sequence of entity 6 (D), FASTA

>7Y65_6 C5a anaphylatoxin chemotactic receptor 1 (chains D)
MDSFNYTTPDYGHYDDKDTLDLNTPVDKTSNTLRVPDILALVIFAVVFLVGVLGNALVVW
VTAFEAKRTINAIWFLNLAVADFLSCLALPILFTSIVQHHHWPFGGAACSILPSLILLNM
YASILLLATISADRFLLVFKPIWCQNFRGAGLAWIACAVAWGLALLLTIPSFLYRVVREE
YFPPKVLCGVDYSHDKRRERAVAIVRLVLGFLWPLLTLTICYTFILLRTWSRRATRSTKT
LKVVVAVVASFFIFWLPYQVTGIMMSFLEPSSPTFLLLKKLDSLCVSFAYINCCINPIIY
VVAGQGFQGRLRKSLPSLLRNVLTEESVVRHHHHHHHHH

Primary citation

Mechanism of activation and biased signaling in complement receptor C5aR1. Feng, Y., Zhao, C., Deng, Y. et al. Cell Res (2023) 33:312-324. DOI 10.1038/s41422-023-00779-2 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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