8JZZ: Human C5a-desArg bound human C5aR1

Structure of human C5a-desArg bound human C5aR1 in complex with Go. Determined by electron microscopy at 3.31 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.31 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,680
Mol. weight: 153.45 kDa
Released: 18 Oct 2023

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

Secondary structure: helices and β-sheets

8JZZ contains 34 α-helices and 68 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: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-52	18
α-helix	55-63	9
α-helix	70-72	3
α-helix	73-87	15
α-helix	89-97	9
α-helix	106-139	34
α-helix	143-145	3
α-helix	150-173	24
β-strand	175-179	5	17
β-strand	186-190	5	17
α-helix	199-207	9
α-helix	208-212	5
α-helix	213-229	17
α-helix	240-267	28
α-helix	273-302	30
α-helix	305-313	9

Chain B: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	31-34	4
α-helix	38-39	2
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	102-105	4	3
β-strand	111-115	5	3
β-strand	120-125	6	3
β-strand	134-140	7	3
β-strand	146-151	6	4
β-strand	157-161	5	4
β-strand	166-168	3	4
β-strand	178-180	3	4
β-strand	187	1	5
β-strand	191-192	2	6
β-strand	198-200	3	6
β-strand	202-203	2	5
β-strand	207-210	4	5
β-strand	211-212	2	6
β-strand	220-222	3	5
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
α-helix	272-273	2
β-strand	278	1	8
β-strand	284-288	5	8
β-strand	294-298	5	8
β-strand	304-307	4	8
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-40	7	9
β-strand	186-191	6	9
β-strand	196-201	6	9
α-helix	202-204	3
α-helix	213-216	4
β-strand	222-227	6	9
α-helix	246-255	10
α-helix	258-260	3
β-strand	265-270	6	9
α-helix	272-281	10
α-helix	297-309	13
β-strand	321-323	3	9
α-helix	331-350	20

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-10	9
α-helix	16-25	10
α-helix	34-39	6
α-helix	45-65	21
β-strand	68	1	17

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	30-43	14

Chain H: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	35-39	5	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-71	4	10
β-strand	79-84	6	10
β-strand	92-94	3	11
β-strand	95-97	3	12
β-strand	111	1	12
β-strand	115-119	5	11
α-helix	138-139	2
β-strand	140-141	2	13
β-strand	146	1	14
β-strand	149	1	15
β-strand	155-161	7	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
β-strand	203-205	3	13
β-strand	208	1	13
β-strand	211-216	6	13
β-strand	226-231	6	14
β-strand	239	1	14
β-strand	243-244	2	14
β-strand	247	1	15

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	C	protein	240	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
C5a anaphylatoxin chemotactic receptor 1	A	protein	406	Homo sapiens	P21730 (AlphaFold model)
C5a anaphylatoxin	D	protein	74	Homo sapiens	P01031

Sequence of entity 1 (B), FASTA

>8JZZ_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 (C), FASTA

>8JZZ_2 Guanine nucleotide-binding protein G(o) subunit alpha (chains C)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGP
NTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 3 (G), FASTA

>8JZZ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (H), FASTA

>8JZZ_4 Antibody fragment ScFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 5 (A), FASTA

>8JZZ_5 C5a anaphylatoxin chemotactic receptor 1 (chains A)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDSF
NYTTPDYGHYDDKDTLDLNTPVDKTSNTLRVPDILALVIFAVVFLVGVLGNALVVWVTAF
EAKRTINAIWFLNLAVADFLSCLALPILFTSIVQHHHWPFGGAACSILPSLILLNMYASI
LLLATISADRFLLVFKPIWCQNFRGAGLAWIACAVAWGLALLLTIPSFLYRVVREEYFPP
KVLCGVDYSHDKRRERAVAIVRLVLGFLWPLLTLTICYTFILLRTWSRRATRSTKTLKVV
VAVVASFFIFWLPYQVTGIMMSFLEPSSPTFLLLKKLDSLCVSFAYINCCINPIIYVVAG
QGFQGRLRKSLPSLLRNVLTEESVVRESKSFTRSTVDTMAQKTQAV

Sequence of entity 6 (D), FASTA

>8JZZ_6 C5a anaphylatoxin (chains D)
TLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQ
LRANISHKDMQLGR

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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