9IJD: PDB entry 9IJD

Carazolol-activated human beta3 adrenergic receptor. Determined by electron microscopy at 2.76 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 2.76 Å
Organisms: Rattus norvegicus, Lama glama, Homo sapiens
Chains: 6
Atoms: 9,371
Mol. weight: 161.5 kDa
Ligands: CAU
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

9IJD contains 34 α-helices and 70 β-strands across 6 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-38	25
β-strand	40-47	8	17
β-strand	208-214	7	17
β-strand	217-223	7	17
α-helix	234-238	5
β-strand	243-248	6	17
α-helix	256-268	13
α-helix	271-274	4
β-strand	276-281	6	17
α-helix	284-292	9
α-helix	298-301	4
α-helix	303-305	3
α-helix	316-317	2
α-helix	322-340	19
β-strand	349-353	5	17
α-helix	361-380	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-151	6	4
β-strand	157-161	5	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	217-223	7	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	249-254	6	6
β-strand	259-264	6	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	53-55	3

Chain D: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
α-helix	53-55	3
β-strand	58-60	3	13
β-strand	68-73	6	11
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	110-111	2	13
β-strand	115-117	3	13
β-strand	118-119	2	12
β-strand	140-142	3	14
β-strand	147-148	2	15
β-strand	155-161	7	14
β-strand	174-179	6	16
β-strand	186-190	5	16
β-strand	194-195	2	16
α-helix	196	1
β-strand	203-208	6	14
β-strand	211-216	6	14
β-strand	225	1	15
β-strand	226-231	6	16
β-strand	239	1	16
β-strand	245-246	2	15

Chain N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	17-25	9	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	46-51	6	10
β-strand	58-60	3	10
β-strand	68-73	6	8
β-strand	78-84	7	8
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	118	1	10
β-strand	122-124	3	10
β-strand	125-126	2	9

Chain R: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	43-64	22
α-helix	72-89	18
α-helix	91-99	9
α-helix	107-140	34
α-helix	142-148	7
α-helix	151-170	20
α-helix	202-209	8
α-helix	210-214	5
α-helix	215-242	28
α-helix	290-318	29
α-helix	325-346	22
α-helix	350-361	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Rattus norvegicus	P54311 (AlphaFold model)
Camelid antibody VHH fragment	N	protein	128	Lama glama
Single-chain Fv16	D	protein	246	Homo sapiens
Beta-3 adrenergic receptor	R	protein	321	Homo sapiens	P13945 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	373	Bos taurus	P04896 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	52	Bos taurus	P63212 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9IJD_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
QSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (N), FASTA

>9IJD_2 Camelid antibody VHH fragment (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSS

Sequence of entity 3 (D), FASTA

>9IJD_3 Single-chain Fv16 (chains D)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSS
GGGGSGGGGSGGGGADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRP
GQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGA
GTKLEL

Sequence of entity 4 (R), FASTA

>9IJD_4 Beta-3 adrenergic receptor (chains R)
ALLALAVLATVGGNLLVIVAIAWTPRLQTMTNVFVTSLAAADLVMGLLVVPPAATLALTG
HWPLGATGCELWTSVDVLCVTASIWTLCALAVDRYLAVTNPLRYGALVTKRCARTAVVLV
WVVSAAVSFAPIMSQWWRVGADAEAQRCHSNPRCCAFASNMPYVLLSSSVSFYLPLLVML
FVYARVFVVATRQLRLLRGELGRFPPEESPPAPSRSLAPAPVGTCAPPEGVPACGRRPAR
LLPLREHRALCTLGLIMGTFTLCWLPFFLANVLRALGGPSLVPGPAFLALNWLGYANSAF
NPLIYCRSPDFRSAFRRLLCR

Sequence of entity 5 (A), FASTA

>9IJD_5 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
LSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHVNGFNGE
GGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELANPENQFRVDYI
LSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDKIDVIKQDDYV
PSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSS
DYNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTP
EDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCRD
IIQRMHLRQYELL

Sequence of entity 6 (C), FASTA

>9IJD_6 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
AQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF

Ligands and cofactors

ID	Name	Formula	Copies
CAU	(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol	C18 H22 N2 O2	1

Primary citation

Molecular Mechanism of the beta 3 AR Agonist Activity of a beta-Blocker. Zheng, S., Zhang, S., Dai, S. et al. Chempluschem (2024) 89:e202400288-e202400288. DOI 10.1002/cplu.202400288 · PubMed

Other PDB entries of the same protein (UniProt P54311 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
9EJZ 2.06 Å, Human M5 muscarinic acetylcholine receptor complex with mini-Gq, agonist acetylcholine…
9IJE 2.34 Å, Epinephrine-activated human beta3 adrenergic receptor
8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
8Z9O 2.4 Å, Cryo-EM structure of human GPR4-Gs complex
22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
7MBY 2.44 Å, Human Cholecystokinin 1 receptor (CCK1R) Gq chimera (mGsqi) complex
9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
8JIS 2.46 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist peptide15-bound human GLP-1R-Gs complex
9M0R 2.47 Å, Structure of neuropeptide FF receptor 1 complex with NPVF
8YKV 2.48 Å, Cryo-EM structure of succinate receptor SUCR1 bound to compound 31
9M1O 2.49 Å, Cryo-EM structures of NPFFR2 complex with neuropeptide FF

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