3GD1: Beta-arrestin-1

Structure of an Arrestin/Clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking. Determined by X-ray diffraction at 3.5 Å resolution. Released 25 Aug 2009.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Bos taurus
Chains: 4
Atoms: 7,854
Mol. weight: 129.9 kDa
Released: 25 Aug 2009

Explore 3GD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GD1 contains 16 α-helices and 88 β-strands across 4 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 C: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	1
β-strand	19-22	4	1
β-strand	26-29	4	2
β-strand	34	1	2
β-strand	37-42	6	1
β-strand	52-63	12	3
β-strand	76-87	12	3
α-helix	99-106	8
β-strand	112-117	6	1
α-helix	124-125	2
β-strand	127-130	4	3
α-helix	136-138	3
β-strand	140-151	12	3
α-helix	157-158	2
β-strand	163-168	6	3
β-strand	169-172	4	2
β-strand	185-187	3	4
β-strand	199-203	5	4
β-strand	207-209	3	5
α-helix	212-213	2
β-strand	214-220	7	4
β-strand	221-222	2	6
β-strand	228-241	14	7
β-strand	245	1	8
β-strand	247-249	3	7
β-strand	252-258	7	7
β-strand	262	1	7
β-strand	266-267	2	6
β-strand	270-274	5	4
β-strand	287-289	3	3
β-strand	300	1	3
α-helix	301-305	5
α-helix	313-315	3
β-strand	317-329	13	7
β-strand	341-349	9	7
β-strand	350-352	3	5
β-strand	387-390	4	1

Chain E: 2 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	9
β-strand	20-22	3	9
β-strand	27-29	3	10
β-strand	34	1	10
β-strand	37-41	5	9
β-strand	56-63	8	11
β-strand	75-80	6	11
β-strand	113-117	5	9
β-strand	128-130	3	11
β-strand	140-148	9	11
β-strand	164-167	4	11
β-strand	170-172	3	10
β-strand	184-187	4	12
β-strand	191	1	8
β-strand	197-203	7	12
β-strand	208-209	2	13
β-strand	214-222	9	12
β-strand	227-241	15	14
β-strand	247-258	12	14
β-strand	262	1	14
β-strand	270-274	5	12
β-strand	287-289	3	11
β-strand	300	1	11
α-helix	313-315	3
β-strand	317-330	14	14
α-helix	336-338	3
β-strand	340-349	10	14
β-strand	351-352	2	13
β-strand	389-390	2	9

Chain I: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	15
α-helix	15-18	4
β-strand	30-31	2	16
β-strand	37-43	7	16
β-strand	48-54	7	16
β-strand	63-65	3	16
β-strand	66	1	17
β-strand	70-73	4	18
β-strand	80-84	5	18
β-strand	87-90	4	18
α-helix	93-95	3
β-strand	100-103	4	18
β-strand	110-115	6	19
β-strand	118-122	5	19
β-strand	126-131	6	19
β-strand	140-143	4	19
α-helix	144-145	2
β-strand	155-158	4	20
β-strand	164-173	10	20
β-strand	176-185	10	20
β-strand	190	1	20
β-strand	193-195	3	20
β-strand	198-204	7	21
β-strand	213-221	9	21
β-strand	226-232	7	21
β-strand	246-249	4	21
β-strand	261-267	7	22
β-strand	272-277	6	22
β-strand	281-286	6	22
β-strand	292-297	6	22
β-strand	303-309	7	15
α-helix	310-312	3
β-strand	314-319	6	15
β-strand	323-329	7	15
α-helix	334-337	4
α-helix	338-342	5
α-helix	345-355	11

Chain Z: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	374	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-arrestin-1	C, E	protein	393	Bos taurus	P17870 (AlphaFold model)
Clathrin heavy chain 1	I	protein	363	Bos taurus	P49951 (AlphaFold model)
clathrin	Z	protein	8	Bos taurus

Sequence of entity 1 (C, E), FASTA

>3GD1_1 Beta-arrestin-1 (chains C, E)
MGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVEPVDGVVLVDPEYLKERRVYVTLTCA
FRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIP
PNLPCSVTLQPGPEDTGKACGVDYEVKAFCAENLEEKIHKRNSVRLVIRKVQYAPERPGP
QPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYAD
ICLFNTAQYKCPVAMEEADDTVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNL
ASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEP
PHREVPEHETPVDTNLIELDTNDDDIVFEDFAR

Sequence of entity 2 (I), FASTA

>3GD1_2 Clathrin heavy chain 1 (chains I)
MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSN
PIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVA
LVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGA
MQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGN
QPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISG
ETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGA
EEL

Sequence of entity 3 (Z), FASTA

>3GD1_3 clathrin (chains Z)
TNLIELDA

Primary citation

Structure of an arrestin2-clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking. Kang, D.S., Kern, R.C., Puthenveedu, M.A. et al. J Biol Chem (2009) 284:29860-29872. DOI 10.1074/jbc.M109.023366 · PubMed

Other PDB entries of the same protein (UniProt P17870 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1G4M 1.9 Å, Crystal structure of bovine beta-arrestin 1
1G4R 2.2 Å, Crystal structure of bovine beta-arrestin 1
3GC3 2.2 Å, Crystal Structure of Arrestin2S and Clathrin
7DFC 2.49 Å, Crystal of Arrestin2-V2Rpp-3-Fab30 complex
7DFA 2.54 Å, Crystal of Arrestin2-V2Rpp-4-Fab30 complex
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
9WSV 2.8 Å, Cryo-EM structure of DAMGO-muOR-arrestin-1-Fab30 complex
9WSX 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-arrestin2-Fab30 complex
22GK 2.84 Å, C5a bound C5aR2 in complex with beta-arrestin1
1JSY 2.9 Å, Crystal structure of bovine arrestin-2
1ZSH 2.9 Å, Crystal structure of bovine arrestin-2 in complex with inositol hexakisphosphate (IP6)
22CR 2.9 Å, C5a-desArg bound C5aR2 in complex with beta-arrestin1

Browse structure collections

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