8XVJ: ETAR

Cryo-EM structure of ETAR bound with Macitentan. Determined by electron microscopy at 3.26 Å resolution. Released 28 Aug 2024.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Homo sapiens, synthetic construct, Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Chains: 4
Atoms: 7,431
Mol. weight: 158.9 kDa
Ligands: A1D5I
Released: 28 Aug 2024

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

Secondary structure: helices and β-sheets

8XVJ contains 32 α-helices and 54 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 H: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14-15	2	2
β-strand	20-28	9	1
α-helix	32-34	3
β-strand	36-42	7	3
β-strand	48-55	8	3
β-strand	60-63	4	3
α-helix	65-67	3
β-strand	71-76	6	1
β-strand	81-87	7	1
α-helix	91-93	3
β-strand	95-102	8	3
α-helix	108-111	4
β-strand	117	1	3
β-strand	121-123	3	3
β-strand	124-125	2	2
β-strand	134-138	5	4
β-strand	152-159	8	4
β-strand	165-168	4	5
α-helix	169-171	3
β-strand	177-179	3	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-196	7	4
β-strand	210-214	5	5
β-strand	219-223	5	5

Chain K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	58-60	3	7
β-strand	69-73	5	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	7
β-strand	108-111	4	7
β-strand	115-119	5	7

Chain L: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	8
β-strand	11-13	3	9
β-strand	20-26	7	8
β-strand	34-39	6	9
β-strand	46-49	4	9
β-strand	55	1	9
β-strand	63-68	6	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	86-94	9	9
β-strand	97-100	4	9
β-strand	104-107	4	9
β-strand	113	1	10
α-helix	114-115	2
β-strand	116-120	5	11
α-helix	121-123	3
α-helix	124-129	6
β-strand	132-141	10	11
β-strand	142	1	10
β-strand	146-152	7	12
β-strand	155-156	2	12
β-strand	161-165	5	11
β-strand	175-183	9	11
α-helix	185-190	6
β-strand	194-200	7	12
β-strand	207-211	5	12

Chain R: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	77-107	31
α-helix	114-132	19
α-helix	134-142	9
α-helix	153-156	4
α-helix	160-186	27
α-helix	200-216	17
α-helix	218-221	4
β-strand	224-231	8	13
β-strand	234-241	8	13
α-helix	246-251	6
α-helix	255-260	6
α-helix	261-265	5
α-helix	266-1023	39
α-helix	1028-1047	20
α-helix	1066-1086	21
α-helix	1090-1097	8
α-helix	1099-1102	4
α-helix	1103-1107	5
α-helix	1108-331	44
α-helix	340-370	31
α-helix	376-381	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-BRIL Fab Heavy chain	H	protein	266	Homo sapiens
anti-Fab Nanobody	K	protein	136	synthetic construct
anti-BRIL Fab Light chain	L	protein	235	Homo sapiens
Endoglucanase H,Endothelin-1 receptor,Soluble cytochrome b562	R	protein	783	Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372), Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P16218 (AlphaFold model), P25101 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8XVJ_1 anti-BRIL Fab Heavy chain (chains H)
MGWSCIILFLVATATGVHSEISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVR
QAPGKGLEWVAYISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAR
WGYWPGEPWWKAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSCDKTHENLYFQGHHHHHH

Sequence of entity 2 (K), FASTA

>8XVJ_2 anti-Fab Nanobody (chains K)
HHHHHHGENLYFQGSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKER
EFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYS
GSYDYWGQGTQVTVSS

Sequence of entity 3 (L), FASTA

>8XVJ_3 anti-BRIL Fab Light chain (chains L)
MGWSCIILFLVATATGVHSSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKP
GKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFG
QGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (R), FASTA

>8XVJ_4 Endoglucanase H,Endothelin-1 receptor,Soluble cytochrome b562 (chains R)
MKTIIALSYIFCLVFADYKDDDDAHHHHHHHHHHGRAMASNYNSGLKIGAWVGTQPSESA
IKSFQELQGRKLDIVHQFINWSTDFSWVRPYADAVYNNGSILMITWEPWEYNTVDIKNGK
ADAYITRMAQDMKAYGKEIWLRPLHAANGDWYPWAIGYSSRVNTNETYIAAFRHIVDIFR
ANGATNVKWVFNVNCDNVGNGTSYLGHYPGDNYVDYTSIDGYNWGTTQSWGSQWQSFDQV
FSRAYQALASINKPIIIAEFASAEIGGNKARWITEAYNSIRTSYNKVIAAVWFHENKETD
WRINSSPEALAAYREAIGAENLYFQGTTHQPTNLVLPSNGSMHNYCPQQTKITSAFKYIN
TVISCTIFIVGMVGNATLLRIIYQNKCMRNGPNALIASLALGDLIYVVIDLPINVFKLLA
GRWPFDHNDFGVFLCKLFPFLQKSSVGITVLNLCALSVDRYRAVASWSRVQGIGIPLVTA
IEIVSIWILSFILAIPEAIGFVMVPFEYRGEQHKTCMLNATSKFMEFYQDVKDWWLFGFY
FCMPLVCTAIFYTLMTCEARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAA
LDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTT
RNAYIQKYLERARSTLKQRREVAKTVFCLVVIFALCWFPLHLSRILKKTVYNEMDKNRCE
LLSFLLLMDYIGINLATMNSCINPIALYFVSKKFKNCFQSCLCCCCYQSKSLMTSVPMNG
TSI

Ligands and cofactors

ID	Name	Formula	Copies
A1D5I	Macitentan	C19 H20 Br2 N6 O4 S	1

Primary citation

Structural basis of antagonist selectivity in endothelin receptors. Hou, J., Liu, S., Zhang, X. et al. Cell Discov (2024) 10:79-79. DOI 10.1038/s41421-024-00705-9 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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