9KYU: Beta-arrestin1

Structure of beta-arrestin1 in complex with mouse C5aR1pp. Determined by electron microscopy at 2.72 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 2.72 Å
Organisms: Rattus norvegicus, Mus musculus
Chains: 8
Atoms: 8,834
Mol. weight: 198.02 kDa
Released: 26 Nov 2025

Explore 9KYU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KYU contains 22 α-helices and 101 β-strands across 8 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, 27 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	1
β-strand	19-22	4	1
β-strand	26-28	3	2
β-strand	29	1	3
β-strand	34	1	3
β-strand	37-42	6	1
α-helix	45-48	4
β-strand	52-62	11	4
β-strand	77-87	11	4
α-helix	96-98	3
α-helix	99-108	10
β-strand	112-117	6	1
β-strand	127-129	3	4
α-helix	130-132	3
β-strand	140-151	12	4
α-helix	157-159	3
β-strand	164-168	5	4
β-strand	169-171	3	2
α-helix	180-182	3
β-strand	183-188	6	5
β-strand	197-203	7	5
β-strand	207-209	3	6
β-strand	214-222	9	5
β-strand	228-242	15	7
β-strand	246-258	13	7
β-strand	262	1	7
β-strand	266-274	9	5
β-strand	288-290	3	4
α-helix	291-292	2
β-strand	300	1	4
α-helix	301-305	5
β-strand	312	1	8
β-strand	316-329	14	7
β-strand	342-349	8	7
β-strand	350-352	3	6
α-helix	354-356	3

Chain D: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	15
β-strand	19-22	4	15
β-strand	26-28	3	16
β-strand	29	1	17
β-strand	34	1	17
β-strand	37-42	6	15
β-strand	52-61	10	18
β-strand	77-87	11	18
α-helix	96-98	3
α-helix	99-108	10
β-strand	112-117	6	15
β-strand	127-129	3	18
α-helix	130-132	3
β-strand	141-151	11	18
α-helix	157-159	3
β-strand	164-168	5	18
β-strand	169-171	3	16
β-strand	183-188	6	8
β-strand	197-203	7	8
β-strand	207-209	3	19
β-strand	214-222	9	8
β-strand	228-242	15	20
β-strand	246-258	13	20
β-strand	262	1	20
β-strand	266-274	9	8
β-strand	288-290	3	18
α-helix	291-292	2
β-strand	300	1	18
α-helix	301-304	4
β-strand	312	1	5
β-strand	316-329	14	20
β-strand	342-349	8	20
β-strand	350-352	3	19
α-helix	354-356	3

Chain I: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	9
β-strand	14	1	10
β-strand	21-28	8	9
β-strand	35-42	8	11
β-strand	48-55	8	11
β-strand	60-63	4	11
β-strand	71-76	6	9
β-strand	81-86	6	9
α-helix	91-93	3
β-strand	95-97	3	12
β-strand	98-103	6	11
β-strand	112-113	2	11
β-strand	117-119	3	12
β-strand	120	1	10

Chain M: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	13
β-strand	11-13	3	14
β-strand	20-26	7	13
β-strand	34-39	6	14
β-strand	46-50	5	14
β-strand	54-55	2	14
α-helix	56	1
β-strand	63-68	6	13
β-strand	71-76	6	13
α-helix	81-83	3
β-strand	86-91	6	14
α-helix	97	1
β-strand	98-99	2	14
β-strand	103-106	4	14

Chain Q: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	23
β-strand	11-13	3	24
β-strand	20-26	7	23
β-strand	34-39	6	24
β-strand	46-50	5	24
β-strand	54-55	2	24
β-strand	63-68	6	23
β-strand	71-76	6	23
β-strand	86-91	6	24
α-helix	97	1
β-strand	98-99	2	24
β-strand	103-106	4	24

Chain R: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	21
β-strand	21-28	8	21
β-strand	35-42	8	22
β-strand	48-55	8	22
β-strand	60-63	4	22
β-strand	71-76	6	21
β-strand	81-86	6	21
α-helix	91-93	3
β-strand	95-103	9	22
β-strand	112-113	2	22
β-strand	117-119	3	22

Chains U and X: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	341-344	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-arrestin-1	A, D	protein	418	Rattus norvegicus	P29066 (AlphaFold model)
C5aR1 phosphopeptide	U, X	protein	23	Mus musculus	P30993 (AlphaFold model)
Fab30 Heavy Chain	I, R	protein	237	Mus musculus
Fab30 Light Chain	M, Q	protein	215	Mus musculus

Sequence of entity 1 (A, D), FASTA

>9KYU_1 Beta-arrestin-1 (chains A, D)
MGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTCA
FRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIP
PNLPCSVTLQPGPEDTGKACGVDYEVKAFCAENLEEKIHKRNSVRLVIRKVQYAPERPGP
QPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYAD
ICLFNTAQYKCPVAMEEADDTVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNL
ASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEP
PHREVPESETPVDTNLIELDTNDDDIVFEDFARQRLKGMKDDKDEEDDGTGSPHLNNR

Sequence of entity 2 (U, X), FASTA

>9KYU_2 C5aR1 phosphopeptide (chains U, X)
GGGDSKTFTPSTTDTSTRKSQAV

Sequence of entity 3 (I, R), FASTA

>9KYU_3 Fab30 Heavy Chain (chains I, R)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYGY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHHH

Sequence of entity 4 (M, Q), FASTA

>9KYU_4 Fab30 Light Chain (chains M, Q)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYKYVPVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Molecular fingerprints of a convergent mechanism orchestrating diverse ligand recognition and species-specific pharmacology at the complement anaphylatoxin receptors. Mishra, S., Yadav, M.K., Dalal, A. et al. bioRxiv (2025). DOI 10.1101/2025.05.26.656101 · PubMed

Other PDB entries of the same protein (UniProt P29066 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JQI 2.6 Å, Structure of active beta-arrestin1 bound to a G protein-coupled receptor phosphopeptide
8HST 2.66 Å, The structure of rat beta-arrestin1
6KL7 2.79 Å, Beta-arrestin 1 mutant S13D/T275D
8HSV 3.0 Å, The structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide
8I0N 3.26 Å, Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human…
9BT8 3.34 Å, Structure of Src in complex with beta-arrestin 1 revealing SH3 binding sites
9CX9 3.34 Å, Structure of SH3 domain of Src in complex with beta-arrestin 1
8J8Z 3.4 Å, Structure of beta-arrestin1 in complex with D6Rpp
8GO8 3.41 Å, Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human…
9CX3 3.47 Å, Structure of SH3 domain of Src in complex with beta-arrestin 1
9DNM 3.47 Å, Structure of rat beta-arrestin 1 bound to allosteric inhibitor
9DNG 3.52 Å, Structure of rat beta-arrestin 1 by fiducial-assisted cryo-EM

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