8HBD: IRL1620-bound ETBR-Gi complex

Cryo-EM structure of IRL1620-bound ETBR-Gi complex. Determined by electron microscopy at 2.99 Å resolution. Released 22 Mar 2023.

Method: Electron microscopy
Resolution: 2.99 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,803
Mol. weight: 189.44 kDa
Released: 22 Mar 2023

Explore 8HBD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HBD contains 36 α-helices and 60 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
β-strand	34-40	7	1
α-helix	47-50	4
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-231	5
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	331-351	21

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	16-25	10
α-helix	30-32	3
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	102-105	4	4
β-strand	111-115	5	4
β-strand	121-125	5	4
β-strand	134-137	4	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	189-192	4	6
β-strand	198-202	5	6
β-strand	208-212	5	6
β-strand	221-222	2	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	260-265	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	293-298	6	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain H: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	110-111	2	10
β-strand	115-119	5	10
β-strand	140	1	11
β-strand	146-148	3	12
β-strand	155-160	6	13
β-strand	161	1	11
β-strand	166	1	14
β-strand	172	1	14
β-strand	176-179	4	12
β-strand	186-190	5	12
β-strand	194-195	2	12
β-strand	204-207	4	13
β-strand	211-216	6	13
α-helix	221-223	3
β-strand	226-229	4	12
β-strand	243-246	4	12

Chain L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	99-128	30
α-helix	135-148	14
α-helix	155-164	10
α-helix	177-204	28
α-helix	216-232	17
α-helix	234-236	3
β-strand	240-246	7	15
β-strand	251-257	7	15
α-helix	264-271	8
α-helix	273-279	7
α-helix	283-296	14
α-helix	297-301	5
α-helix	312-348	37
α-helix	357-379	23
α-helix	381-388	8
α-helix	393-398	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	377	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	H	protein	285	Mus musculus
IRL1620	L	protein	15	Homo sapiens
Endothelin receptor type B,Endothelin receptor type B,Oplophorus-luciferin 2-monooxygenase…	R	protein	603	Homo sapiens	P24530 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8HBD_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8HBD_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS

Sequence of entity 3 (G), FASTA

>8HBD_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (H), FASTA

>8HBD_4 scFv16 (chains H)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 5 (L), FASTA

>8HBD_5 IRL1620 (chains L)
DDEEAVYFAHLDIIW

Sequence of entity 6 (R), FASTA

>8HBD_6 Endothelin receptor type B,Endothelin receptor type B,Oplophorus-luciferin 2-monooxygenase catalytic subunit chimera (chains R)
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSDYKDDDDVDHHHHHHHHEERGFPPDRATPL
LQTAEIMTPPTKTLWPKGSNASLARSLAPAEVPKGDRTAGSPPRTISPPPCQGPIEIKET
FKYINTVVSCLVFVLGIIGNSTLLRIIYKNKCMRNGPNILIASLALGDLLHIVIDIPINV
YKLLAEDWPFGAEMCKLVPFIQKASVGITVLSLCALSIDRYRAVASWSRIKGIGVPKWTA
VEIVLIWVVSVVLAVPEAIGFDIITMDYKGSYLRICLLHPVQKTAFMQFYKTAKDWWLFS
FYFCLPLAITAFFYTLMTCEMLRKKSGMQIALNDHLKQRREVAKTVFCLVLVFALCWLPL
HLSRILKLTLYNQNDPNRCELLSFLLVLDYIGINMASLNSCINPIALYLVSKRFKNCFKS
CLCCWCQSFEEKQSLEEKQSCLKFKVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNL
AVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPY
GTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVT
INS

Primary citation

Structural basis of peptide recognition and activation of endothelin receptors. Ji, Y., Duan, J., Yuan, Q. et al. Nat Commun (2023) 14:1268-1268. DOI 10.1038/s41467-023-36998-9 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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