6IBL: Thioredoxin 1,Beta-1 adrenergic receptor

Activated turkey BETA1 adrenoceptor with bound agonist formoterol and nanobody Nb80. Determined by X-ray diffraction at 2.7 Å resolution. Released 9 Jan 2019.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Escherichia coli (strain K12), Meleagris gallopavo, Lama glama
Chains: 4
Atoms: 8,271
Mol. weight: 123.39 kDa
Ligands: 2CV, H98
Released: 9 Jan 2019

Explore 6IBL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IBL contains 45 α-helices and 33 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 A: 19 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	1005-1006	2	1
α-helix	1012	1
α-helix	1013-1017	5
β-strand	1022-1028	7	1
α-helix	1033-1048	16
β-strand	1054-1059	6	1
α-helix	1067-1070	4
β-strand	1077-1082	6	1
β-strand	1086-1088	3	1
α-helix	1096-1107	12
α-helix	42-68	27
α-helix	75-89	15
α-helix	90-94	5
α-helix	95-104	10
α-helix	110-144	35
α-helix	146-152	7
α-helix	155-178	24
α-helix	187-194	8
α-helix	205-212	8
α-helix	213-217	5
α-helix	218-243	26
α-helix	283-315	33
α-helix	322-343	22
α-helix	347-356	10

Chain B: 20 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	1005-1006	2	4
α-helix	1011-1012	2
α-helix	1013-1017	5
β-strand	1022-1028	7	4
α-helix	1033-1036	4
α-helix	1039-1048	10
β-strand	1054-1059	6	4
α-helix	1068-1070	3
β-strand	1077-1082	6	4
β-strand	1086-1091	6	4
α-helix	1096-1107	12
α-helix	42-68	27
α-helix	76-89	14
α-helix	90-94	5
α-helix	95-104	10
α-helix	110-144	35
α-helix	146-152	7
α-helix	155-178	24
α-helix	187-194	8
α-helix	205-212	8
α-helix	213-217	5
α-helix	218-272	27
α-helix	283-315	33
α-helix	322-343	22
α-helix	347-356	10

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	10-13	4	3
β-strand	18-25	8	2
β-strand	32-39	8	3
β-strand	46-52	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-71	5	2
β-strand	77-82	6	2
α-helix	87-89	3
β-strand	91-99	9	3
α-helix	106	1
β-strand	107-110	4	3
β-strand	114-119	6	3

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	11-13	3	6
β-strand	18-25	8	5
β-strand	32-39	8	7
β-strand	46-52	7	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	67-71	5	5
β-strand	77-82	6	5
α-helix	87-89	3
β-strand	91-99	9	7
α-helix	106	1
β-strand	107-110	4	7
β-strand	114-116	3	7
β-strand	117-119	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thioredoxin 1,Beta-1 adrenergic receptor	A, B	protein	416	Escherichia coli (strain K12), Meleagris gallopavo	P07700 (AlphaFold model), P0AA25 (AlphaFold model)
Camelid antibody fragment Nb80	C, D	protein	121	Lama glama

Sequence of entity 1 (A, B), FASTA

>6IBL_1 Thioredoxin 1,Beta-1 adrenergic receptor (chains A, B)
SDKIIHLTDDSFDTDVLKADGAILVDFWAEWSGPSKMIAPILDEIADEYQGKLTVAKLNI
DQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAEAAAKVMSLLMA
LVVLLIVAGNVLVIAAIGSTQRLQTLTNLFITSLACADLVVGLLVVPFGATLVVRGTWLW
GSFLCELWTSLDVLCVTASIETLCVIAIDRYLAITSPFRYQSLMTRARAKVIICTVWAIS
ALVSFLPIMMHWWRDEDPQALKCYQDPGCCDFVTNRAYAIASSIISFYIPLLIMIFVYLR
VYREAKEQIRKIDRASKRKTSRVMAMKEHKALKTLGIIMGVFTLCWLPFFLVNIVNVFNR
DLVPDWLFVAFNWLGYANSAMNPIIYCRSPDFRKAFKRLLAFPRKADRRLHHHHHH

Sequence of entity 2 (C, D), FASTA

>6IBL_2 Camelid antibody fragment Nb80 (chains C, D)
SQVQLQESGGGLVQAGGSLRLSCAASGSIFSINTMGWYRQAPGKQRELVAAIHSGGSTNY
ANSVKGRFTISRDNAANTVYLQMNSLKPEDTAVYYCNVKDYGAVLYEYDYWGQGTQVTVS
S

Ligands and cofactors

ID	Name	Formula	Copies
2CV	Hega-10	C18 H37 N O7	8
H98	~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-e…	C19 H24 N2 O4	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Molecular basis of beta-arrestin coupling to formoterol-bound beta1-adrenoceptor. Lee, Y., Warne, T., Nehme, R. et al. Nature (2020) 583:862-866. DOI 10.1038/s41586-020-2419-1 · PubMed

Other PDB entries of the same protein (UniProt P07700 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4BVN 2.1 Å, Ultra-thermostable beta1-adrenoceptor with cyanopindolol bound
4AMJ 2.3 Å, Turkey beta1 adrenergic receptor with stabilising mutations and bound biased agonist…
5A8E 2.4 Å, thermostabilised beta1-adrenoceptor with rationally designed inverse agonist…
2Y00 2.5 Å, Turkey BETA1 adrenergic receptor with stabilising mutations and bound partial agonist…
6H7N 2.5 Å, Activated turkey BETA1 adrenoceptor with bound partial agonist xamoterol and nanobody…
8DCS 2.5 Å, Cryo-EM structure of cyanopindolol-bound beta1-adrenergic receptor in complex with…
2Y01 2.6 Å, Turkey BETA1 adrenergic receptor with stabilising mutations and bound partial agonist…
2Y02 2.6 Å, Turkey BETA1 adrenergic receptor with stabilising mutations and bound agonist carmoterol
7JJO 2.6 Å, Structural Basis of the Activation of Heterotrimeric Gs-protein by Isoproterenol-bound…
8DCR 2.6 Å, Cryo-EM structure of dobutamine-bound beta1-adrenergic receptor in complex with…
2VT4 2.7 Å, Turkey BETA1 adrenergic receptor with stabilising mutations and bound cyanopindolol
3ZPR 2.7 Å, Thermostabilised turkey beta1 adrenergic receptor with 4-methyl-2-(piperazin-1-yl)…

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