8HK5: C5aR1-Gi-C5a protein complex

C5aR1-Gi-C5a protein complex. Determined by electron microscopy at 3.0 Å resolution. Released 10 May 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 5
Atoms: 7,604
Mol. weight: 133.84 kDa
Ligands: PLM
Released: 10 May 2023

Explore 8HK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HK5 contains 33 α-helices and 39 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-65	31
α-helix	71-87	17
α-helix	89-97	9
α-helix	108-139	32
α-helix	141-147	7
α-helix	150-174	25
β-strand	175-180	6	1
β-strand	185-191	7	1
α-helix	196-207	12
α-helix	208-212	5
α-helix	213-230	18
α-helix	238-265	28
α-helix	273-289	17
α-helix	291-303	13
α-helix	307-313	7

Chain B: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	16-26	11
α-helix	34-39	6
α-helix	45-62	18
β-strand	67-69	3	1

Chain C: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-32	27
β-strand	34-40	7	2
α-helix	46-52	7
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	227-231	5
β-strand	233	1	3
β-strand	241	1	3
α-helix	242-254	13
β-strand	263-269	7	2
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	2
α-helix	331-350	20

Chain D: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	14-25	12
α-helix	30-33	4
α-helix	38-42	5
α-helix	45-46	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	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	165-170	6	7
β-strand	175-181	7	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	218-222	5	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 G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	17-24	8
α-helix	30-43	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C5a anaphylatoxin chemotactic receptor 1	A	protein	350	Homo sapiens	P21730 (AlphaFold model)
Complement C5	B	protein	74	Homo sapiens	P01031 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	353	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D	protein	345	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein subunit gamma	G	protein	67	Bos taurus	P63212

Sequence of entity 1 (A), FASTA

>8HK5_1 C5a anaphylatoxin chemotactic receptor 1 (chains A)
MDSFNYTTPDYGHYDDKDTLDLNTPVDKTSNTLRVPDILALVIFAVVFLVGVLGNALVVW
VTAFEAKRTINAIWFLNLAVADFLSCLALPILFTSIVQHHHWPFGGAACSILPSLILLNM
YASILLLATISADRFLLVFKPIWCQNFRGAGLAWIACAVAWGLALLLTIPSFLYRVVREE
YFPPKVLCGVDYSHDKRRERAVAIVRLVLGFLWPLLTLTICYTFILLRTWSRRATRSTKT
LKVVVAVVASFFIFWLPYQVTGIMMSFLEPSSPTFLLLKKLDSLCVSFAYINCCINPIIY
VVAGQGFQGRLRKSLPSLLRNVLTEESVVRESKSFTRSTVDTMAQKTQAV

Sequence of entity 2 (B), FASTA

>8HK5_2 Complement C5 (chains B)
TLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQ
LRANISHKDMQLGR

Sequence of entity 3 (C), FASTA

>8HK5_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (D), FASTA

>8HK5_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains D)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>8HK5_5 Guanine nucleotide-binding protein subunit gamma (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	2

Primary citation

Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins. Wang, Y., Liu, W., Xu, Y. et al. Nat Chem Biol (2023) 19:1351-1360. DOI 10.1038/s41589-023-01339-w · 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
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
8IA2 3.21 Å, Structure of C5a bound human C5aR1 in complex with Go (Composite map)

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