8XWP: ET-1 bound ETBR-DNGI complex

Cryo-EM structure of ET-1 bound ETBR-DNGI complex. Determined by electron microscopy at 3.21 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 9,076
Mol. weight: 156.65 kDa
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

8XWP contains 31 α-helices and 65 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	35-40	6	3
α-helix	46-52	7
β-strand	185-188	4	3
β-strand	197-200	4	3
β-strand	220-226	7	3
α-helix	227-229	3
α-helix	242-254	13
β-strand	263-269	7	3
α-helix	271-280	10
α-helix	296-308	13
β-strand	319-320	2	3
α-helix	330-351	22

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	31-34	4
α-helix	38-39	2
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	88-94	7	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	157-161	5	7
β-strand	165-168	4	7
β-strand	178-181	4	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	218-222	5	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	252-254	3	9
β-strand	259-262	4	9
β-strand	273-277	5	10
β-strand	286-289	4	10
β-strand	294-296	3	10
β-strand	307-308	2	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain C: 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 D: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	12	1	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-84	7	11
β-strand	93-99	7	13
β-strand	110-111	2	13
β-strand	115	1	13
β-strand	119	1	12
β-strand	128-129	2	14
β-strand	134-136	3	15
β-strand	143-147	5	16
β-strand	148-149	2	14
β-strand	154	1	17
β-strand	160	1	17
β-strand	162-167	6	15
β-strand	174-178	5	15
β-strand	182-183	2	15
α-helix	184	1
β-strand	194-196	3	16
β-strand	199-204	6	16
β-strand	214-219	6	15
α-helix	226	1
β-strand	227	1	15
α-helix	228	1
β-strand	231-234	4	15

Chain L: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	11-17	7

Chain R: 11 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	98-128	31
α-helix	135-160	26
α-helix	171-204	34
α-helix	218-237	20
β-strand	240-243	4	1
β-strand	246-247	2	2
β-strand	250-251	2	2
β-strand	254-257	4	1
α-helix	264-271	8
α-helix	273-277	5
α-helix	278-283	6
α-helix	284-300	17
α-helix	313-348	36
α-helix	357-387	31
α-helix	391-398	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endothelin receptor type B	R	protein	346	Homo sapiens	P24530 (AlphaFold model)
Endothelin-1	L	protein	21	Homo sapiens	P05305 (AlphaFold model)
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	344	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768
SCFV16	D	protein	277	Mus musculus

Sequence of entity 1 (R), FASTA

>8XWP_1 Endothelin receptor type B (chains R)
PGGGLAPAEVPKGDRTAGSPPRTISPPPCQGPIEIKETFKYINTVVSCLVFVLGIIGNST
LLYIIYKNKCMRNGPNILIASLALGDLLHIVIDIPINVYKLLAEDWPFGAEMCKLVPFIQ
KASVGITVLSLCALSIDRYRAVASWSRIKGIGVPKWTAVEIVLIWVVSVVLAVPEAIGFD
IITMDYKGSYLRICLLHPVQKTAFMQFYKTAKDWWLFSFYFCLPLAITAFFYTLMTCEML
RKKSGMQIALNDHLKQRREVAKTVFCLVLVFALCWLPLHLSRILKLTLYNQNDPNRCELL
SFLLVLDYIGINMASLNSCINPIALYLVSKRFKNAFKSALCCWAQS

Sequence of entity 2 (L), FASTA

>8XWP_2 Endothelin-1 (chains L)
CSCSSLMDKECVYFCHLDIIW

Sequence of entity 3 (A), FASTA

>8XWP_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>8XWP_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
PGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (C), FASTA

>8XWP_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (D), FASTA

>8XWP_6 SCFV16 (chains D)
MVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQA
PEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSI
YYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCR
SSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLE
AEDVGVYYCMQHLEYPLTFGAGTKLELKGSLEVLFQG

Primary citation

Structure of endothelin ET B receptor-G i complex in a conformation stabilized by unique NPxxL motif. Tani, K., Maki-Yonekura, S., Kanno, R. et al. Commun Biol (2024) 7:1303-1303. DOI 10.1038/s42003-024-06905-z · PubMed

Other PDB entries of the same protein (UniProt P24530 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6IGK 2.0 Å, Crystal Structure of human ETB receptor in complex with Endothelin-3
5X93 2.2 Å, Human endothelin receptor type-B in complex with antagonist K-8794
5GLI 2.5 Å, Human endothelin receptor type-B in the ligand-free form
6IGL 2.7 Å, Crystal Structure of human ETB receptor in complex with IRL1620
6K1Q 2.7 Å, Human endothelin receptor type-B in complex with inverse agonist IRL2500
5GLH 2.8 Å, Human endothelin receptor type-B in complex with ET-1
8IY5 2.8 Å, ETB-Gi complex bound to endothelin-1
8HBD 2.99 Å, Cryo-EM structure of IRL1620-bound ETBR-Gi complex
6LRY 3.0 Å, Crystal structure of human endothelin ETB receptor in complex with sarafotoxin S6b
8XVE 3.0 Å, Cryo-EM structure of ETBR bound with BQ3020
8IY6 3.13 Å, ETB-Gi complex bound to Endotheline-1, focused on receptor
8XGR 3.2 Å, ETB-eGt complex bound to endothelin-1

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