8HPT: C5a-pep bound mouse C5aR1

Structure of C5a-pep bound mouse C5aR1 in complex with Go. Determined by electron microscopy at 3.39 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.39 Å
Organisms: Mus musculus, synthetic construct, Homo sapiens
Chains: 6
Atoms: 7,897
Mol. weight: 143.55 kDa
Released: 18 Oct 2023

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

Secondary structure: helices and β-sheets

8HPT contains 36 α-helices and 63 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	37-62	26
α-helix	71-86	16
α-helix	89-97	9
α-helix	107-109	3
α-helix	112-139	28
α-helix	143-146	4
α-helix	150-173	24
α-helix	202-208	7
α-helix	209-213	5
α-helix	214-230	17
α-helix	234-236	3
α-helix	240-265	26
α-helix	277-304	28
α-helix	306-314	9

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-38	5	1
α-helix	46-52	7
β-strand	186-191	6	1
β-strand	196-201	6	1
α-helix	209-212	4
α-helix	213-216	4
β-strand	221-227	7	1
α-helix	246-255	10
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	297-309	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain C: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69	1	4
β-strand	70-74	5	3
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187	1	7
β-strand	191-192	2	8
β-strand	199-202	4	8
β-strand	203	1	7
β-strand	208-210	3	8
β-strand	220-222	3	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	249-254	6	9
β-strand	259-265	7	9
α-helix	272	1
β-strand	273-277	5	10
β-strand	284-289	6	10
β-strand	293-298	6	10
β-strand	303-309	7	10
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	54-55	2

Chain H: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	70-73	4	11
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	93-98	6	13
β-strand	111	1	13
β-strand	115-116	2	13
β-strand	117-119	3	12
β-strand	141	1	14
β-strand	146-149	4	15
β-strand	155-160	6	14
β-strand	166	1	16
β-strand	172	1	16
β-strand	175-179	5	15
β-strand	186-190	5	15
β-strand	194-195	2	15
α-helix	196	1
β-strand	203-208	6	14
β-strand	211-216	6	14
α-helix	221-223	3
β-strand	226-230	5	15
β-strand	231	1	17
α-helix	237	1
β-strand	238	1	17
β-strand	243-247	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C5a anaphylatoxin chemotactic receptor 1	A	protein	407	Mus musculus	P30993 (AlphaFold model)
Mea-lys-pro-zal-alc-dar	D	protein	6	synthetic construct
Guanine nucleotide-binding protein G(o) subunit alpha	B	protein	240	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	338	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	56	Homo sapiens	P59768 (AlphaFold model)
Antibody fragment ScFv16	H	protein	256	Mus musculus

Sequence of entity 1 (A), FASTA

>8HPT_1 C5a anaphylatoxin chemotactic receptor 1 (chains A)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDPI
DNSSFEINYDHYGTMDPNIPADGIHLPKRQPGDVAALIIYSVVFLVGVPGNALVVWVTAF
EARRAVNAIWFLNLAVADLLSCLALPVLFTTVLNHNYWYFDATACIVLPSLILLNMYASI
LLLATISADRFLLVFKPIWCQKVRGTGLAWMACGVAWVLALLLTIPSFVYREAYKDFYSE
HTVCGINYGGGSFPKEKAVAILRLMVGFVLPLLTLNICYTFLLLRTWSRKATRSTKTLKV
VMAVVICFFIFWLPYQVTGVMIAWLPPSSPTLKRVEKLNSLCVSLAYINCCVNPIIYVMA
GQGFHGRLLRSLPSIIRNALSEDSVGRDSKTFTPSTTDTSTRKSQAV

Sequence of entity 2 (D), FASTA

>8HPT_2 MEA-LYS-PRO-ZAL-ALC-DAR (chains D)
FKPAAR

Sequence of entity 3 (B), FASTA

>8HPT_3 Guanine nucleotide-binding protein G(o) subunit alpha (chains B)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGP
NTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 4 (C), FASTA

>8HPT_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>8HPT_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 6 (H), FASTA

>8HPT_6 Antibody fragment ScFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

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 P30993 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9KYU 2.72 Å, Structure of beta-arrestin1 in complex with mouse C5aR1pp
9KY2 2.78 Å, Structure of beta-arrestin2 in complex with mouse C5aR1pp
9KX6 3.11 Å, Structure of human C5a-desArg bound mouse C5aR1 in complex with Go
9KWX 3.13 Å, Structure of mouse C5a-desArg bound mouse C5aR1 in complex with Go
9KWG 3.15 Å, Structure of mouse C5a bound mouse C5aR1 in complex with Go
9KXS 3.31 Å, Structure of EP67 bound mouse C5aR1 in complex with Go
8HQC 3.89 Å, Structure of a GPCR-G protein in complex with a natural peptide agonist

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