5O9H: C5a anaphylatoxin chemotactic receptor 1

Crystal structure of thermostabilised human C5a anaphylatoxin chemotactic receptor 1 (C5aR) in complex with NDT9513727. Determined by X-ray diffraction at 2.7 Å resolution. Released 10 Jan 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,349
Mol. weight: 82.31 kDa
Ligands: CIT, OLA, TLA, 9P2
Released: 10 Jan 2018

Explore 5O9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O9H contains 34 α-helices and 4 β-strands across 2 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: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
α-helix	35-63	29
α-helix	70-87	18
α-helix	89-97	9
α-helix	105-111	7
α-helix	112-114	3
α-helix	115-139	25
α-helix	141-147	7
α-helix	150-174	25
β-strand	176-181	6	1
β-strand	184-189	6	1
α-helix	196-207	12
α-helix	208-212	5
α-helix	213-231	19
α-helix	239-266	28
α-helix	273-280	8
α-helix	282-290	9
α-helix	291-293	3
α-helix	295-306	12
α-helix	315-323	9

Chain B: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
α-helix	35-63	29
α-helix	70-86	17
α-helix	89-97	9
α-helix	105-111	7
α-helix	115-139	25
α-helix	141-147	7
α-helix	150-173	24
β-strand	175-181	7	2
β-strand	184-190	7	2
α-helix	198-207	10
α-helix	208-212	5
α-helix	213-231	19
α-helix	239-264	26
α-helix	273-280	8
α-helix	282-289	8
α-helix	292-304	13
α-helix	315-323	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C5a anaphylatoxin chemotactic receptor 1	A, B	protein	317	Homo sapiens	P21730 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5O9H_1 C5a anaphylatoxin chemotactic receptor 1 (chains A, B)
MNTLRVPDILALVIFAVVFLVGVLGNALVVWVTAFEAKRTINAIWFLNLAVADFLACLAL
PALFTSIVQHHHWPFGGAACSILPSLILLNMYASILLLATISADRFLLVFKPAWCQRFRG
AGLAWILCAVAWGLALLLTIPSALYRVVREEYFPPKVLCGVDYSHDKRRERAVAIVRLVL
GFLWPLLTLTICYTFILLRTWSARETRSTKTLKVVVAVVASFFIFWLPYQVTGIMMSFLE
PSSPTFLLLKKLDSLCVSFAYINCCINPIIYVVAGQGFQGRERKSLPELLREVLTEESVV
RESKAAAHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
OLA	Oleic acid	C18 H34 O2	32
TLA	L(+)-tartaric acid	C4 H6 O6	3
9P2	1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-d…	C36 H35 N3 O4	2

Primary citation

Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727. Robertson, N., Rappas, M., Dore, A.S. et al. Nature (2018) 553:111-114. DOI 10.1038/nature25025 · 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
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
8IA2 3.21 Å, Structure of C5a bound human C5aR1 in complex with Go (Composite map)

Browse structure collections

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