9DNM: Rat beta-arrestin 1

Structure of rat beta-arrestin 1 bound to allosteric inhibitor. Determined by electron microscopy at 3.47 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.47 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 3
Atoms: 5,235
Mol. weight: 103.21 kDa
Ligands: ODN
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

9DNM contains 14 α-helices and 54 β-strands across 3 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: 11 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	6
β-strand	18-22	5	6
β-strand	26	1	7
β-strand	29	1	8
β-strand	34	1	8
β-strand	37	1	9
β-strand	40-43	4	6
β-strand	52-61	10	10
β-strand	77-85	9	10
α-helix	99-107	9
β-strand	112-114	3	6
β-strand	117	1	9
β-strand	126-127	2	11
β-strand	141	1	11
β-strand	142-151	10	10
α-helix	160-162	3
β-strand	163-168	6	10
β-strand	169	1	7
α-helix	178-194	17
α-helix	199-218	20
α-helix	222-224	3
α-helix	232-257	26
α-helix	260-267	8
α-helix	270-281	12
β-strand	284-289	6	12
β-strand	298-304	7	12
β-strand	308-310	3	13
β-strand	315-322	8	12
β-strand	329-343	15	14
β-strand	351-357	7	14
β-strand	363	1	14
β-strand	368-375	8	12
α-helix	379-382	4
β-strand	389-390	2	11
β-strand	401	1	11
α-helix	402-408	7
α-helix	413-415	3
β-strand	417-430	14	14
β-strand	444-447	4	14
β-strand	450	1	14
β-strand	451-453	3	13
β-strand	488-491	4	6

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14-15	2	2
β-strand	21-28	8	1
α-helix	32-34	3
β-strand	36-42	7	3
β-strand	48-54	7	3
β-strand	61-63	3	3
β-strand	72-76	5	1
β-strand	81-86	6	1
β-strand	95-102	8	3
β-strand	117	1	3
β-strand	121-123	3	3
β-strand	124-125	2	2

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	4
β-strand	11-13	3	5
β-strand	20-26	7	4
β-strand	34-39	6	5
β-strand	46-50	5	5
β-strand	54-55	2	5
α-helix	56	1
β-strand	63-67	5	4
β-strand	71-76	6	4
α-helix	81-83	3
β-strand	86-91	6	5
β-strand	99-100	2	5
β-strand	104-107	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-BRIL Fab Heavy chain	H	protein	225	Homo sapiens
anti-BRIL Fab Light chain	L	protein	212	Homo sapiens
Beta-arrestin-1,Soluble cytochrome b562	A	protein	494	Rattus norvegicus	P29066 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9DNM_1 anti-BRIL Fab Heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGSTSY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 2 (L), FASTA

>9DNM_2 anti-BRIL Fab Light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 3 (A), FASTA

>9DNM_3 Beta-arrestin-1,Soluble cytochrome b562 (chains A)
LGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTCA
FRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIP
PNLPCSVTLQPGPEDTGKACGVDYEVKAFCAENLEEKIHKRNSVRLVIRKVQYAPEADLE
DNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHG
FDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLPTAETTRQFLMSDKPLHL
EASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADICLFNTAQYKCPVAMEEAD
DTVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLREGANREILGIIV
SYKVKVKLVVSRGDYKDDDDKSDVAVELPFTLMHPKPKEEPPHREVPESETPVDTNLIEL
DTNDDDIVFEDFAR

Ligands and cofactors

ID	Name	Formula	Copies
ODN	(1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydro…	C20 H30 O6	1

Primary citation

Small-molecule modulation of beta-arrestins. Kahsai, A.W., Pakharukova, N., Kwon, H.Y. et al. Nature (2026) 656:770-779. DOI 10.1038/s41586-026-10683-5 · 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
9KYU 2.72 Å, Structure of beta-arrestin1 in complex with mouse C5aR1pp
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
9DNG 3.52 Å, Structure of rat beta-arrestin 1 by fiducial-assisted cryo-EM

Browse structure collections

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