9DNG: Rat beta-arrestin 1 by fiducial-assisted cryo-EM

Structure of rat beta-arrestin 1 by fiducial-assisted cryo-EM. Determined by electron microscopy at 3.52 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.52 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 3
Atoms: 5,252
Mol. weight: 102.84 kDa
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

9DNG contains 20 α-helices and 53 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: 13 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	6
β-strand	19-22	4	6
β-strand	26-28	3	7
α-helix	34-36	3
β-strand	37-42	6	6
β-strand	52-55	4	8
β-strand	56	1	9
β-strand	58-62	5	10
β-strand	83	1	9
α-helix	99-103	5
α-helix	104-106	3
β-strand	113-117	5	6
β-strand	127-129	3	10
β-strand	141-145	5	10
β-strand	146-151	6	8
α-helix	157-158	2
α-helix	160-162	3
β-strand	164-166	3	8
β-strand	169-171	3	7
β-strand	173	1	11
α-helix	179-195	17
α-helix	199-217	19
α-helix	232-257	26
α-helix	260-281	22
β-strand	284-289	6	12
β-strand	298-304	7	12
β-strand	308-310	3	13
β-strand	315-323	9	12
β-strand	332-342	11	14
β-strand	349-359	11	14
β-strand	367-375	9	12
α-helix	379-382	4
β-strand	389-390	2	10
β-strand	401	1	10
α-helix	402-404	3
α-helix	406-408	3
α-helix	414-416	3
β-strand	418-428	11	14
β-strand	445-450	6	14
β-strand	451-453	3	13
β-strand	454	1	11
β-strand	490-491	2	6

Chain H: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14-15	2	2
β-strand	20-28	9	1
α-helix	32-34	3
β-strand	36-42	7	3
β-strand	48-55	8	3
β-strand	60-63	4	3
β-strand	72-76	5	1
α-helix	77-79	3
β-strand	81-87	7	1
α-helix	91-93	3
β-strand	96-102	7	3
α-helix	108-111	4
β-strand	116	1	3
β-strand	118	1	1
β-strand	121-122	2	3
β-strand	124-125	2	2

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	4
β-strand	11-13	3	5
β-strand	19-26	8	4
β-strand	34-39	6	5
β-strand	47-50	4	5
β-strand	54-55	2	5
α-helix	56	1
β-strand	63-68	6	4
β-strand	71-77	7	4
β-strand	86-91	6	5
α-helix	95-97	3
β-strand	99-100	2	5
α-helix	101-103	3
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

>9DNG_1 anti-BRIL Fab Heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGSTSY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 2 (L), FASTA

>9DNG_2 anti-BRIL Fab LIGHT chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 3 (A), FASTA

>9DNG_3 Beta-arrestin-1,Soluble cytochrome b562 (chains A)
LGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTCA
FRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIP
PNLPCSVTLQPGPEDTGKACGVDYEVKAFCAENLEEKIHKRNSVRLVIRKVQYAPEADLE
DNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHG
FDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLPTAETTRQFLMSDKPLHL
EASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADICLFNTAQYKCPVAMEEAD
DTVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLREGANREILGIIV
SYKVKVKLVVSRGDYKDDDDKSDVAVELPFTLMHPKPKEEPPHREVPESETPVDTNLIEL
DTNDDDIVFEDFAR

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
9DNM 3.47 Å, Structure of rat beta-arrestin 1 bound to allosteric inhibitor

Browse structure collections

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