8XVK: ETAR

Cryo-EM structure of ETAR bound with Ambrisentan. Determined by electron microscopy at 3.21 Å resolution. Released 28 Aug 2024.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Homo sapiens, synthetic construct, Acetivibrio thermocellus ATCC 27405
Chains: 4
Atoms: 7,388
Mol. weight: 158.69 kDa
Ligands: A1D5J
Released: 28 Aug 2024

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

Secondary structure: helices and β-sheets

8XVK contains 32 α-helices and 56 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	15	1	2
β-strand	20-22	3	1
β-strand	24-28	5	1
α-helix	32-34	3
β-strand	36-42	7	3
β-strand	48-54	7	3
β-strand	61-63	3	3
β-strand	71-76	6	1
β-strand	81-87	7	1
β-strand	95-102	8	3
α-helix	108-110	3
β-strand	121-123	3	3
β-strand	125	1	2
α-helix	128-130	3
β-strand	134-137	4	4
α-helix	139-141	3
β-strand	152-157	6	4
β-strand	165-167	3	5
β-strand	168	1	6
α-helix	169-171	3
β-strand	173	1	6
β-strand	177-179	3	4
α-helix	181-182	2
β-strand	183	1	4
β-strand	191-196	6	4
β-strand	209-214	6	5
β-strand	219-224	6	5

Chain K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	7
β-strand	17	1	8
β-strand	20-23	4	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	60	1	9
β-strand	70-73	4	7
β-strand	78-81	4	7
β-strand	84	1	8
α-helix	88-90	3
β-strand	92-98	7	9
β-strand	115-117	3	9

Chain L: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	10
β-strand	11-13	3	11
β-strand	20-26	7	10
β-strand	34-39	6	11
β-strand	46-49	4	11
β-strand	55	1	11
β-strand	63-68	6	10
β-strand	71-76	6	10
β-strand	86-91	6	11
β-strand	99-100	2	11
β-strand	104-107	4	11
β-strand	113	1	12
β-strand	120	1	13
α-helix	121-123	3
α-helix	124-129	6
β-strand	131-141	11	13
β-strand	142	1	12
β-strand	146-152	7	14
β-strand	155-156	2	14
β-strand	163-165	3	13
β-strand	175-184	10	13
α-helix	185-190	6
β-strand	193-200	8	14
β-strand	207-212	6	14

Chain R: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	78-107	30
α-helix	114-141	28
α-helix	154-188	35
α-helix	200-222	23
β-strand	225-229	5	15
α-helix	231-233	3
β-strand	236-240	5	15
α-helix	246-253	8
α-helix	256-260	5
α-helix	261-265	5
α-helix	266-268	3
α-helix	270-1022	34
α-helix	1028-1048	21
α-helix	1066-1085	20
α-helix	1089-1097	9
α-helix	1100-1102	3
α-helix	1103-1107	5
α-helix	1108-327	40
α-helix	338-341	4
α-helix	343-359	17
α-helix	360-362	3
α-helix	365-372	8
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 ATCC 27405, Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P16218 (AlphaFold model), P25101 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8XVK_1 anti-BRIL Fab Heavy chain (chains H)
MGWSCIILFLVATATGVHSEISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVR
QAPGKGLEWVAYISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAR
WGYWPGEPWWKAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP
EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DKKVEPKSCDKTHENLYFQGHHHHHH

Sequence of entity 2 (K), FASTA

>8XVK_2 anti-Fab Nanobody (chains K)
HHHHHHGENLYFQGSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKER
EFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYS
GSYDYWGQGTQVTVSS

Sequence of entity 3 (L), FASTA

>8XVK_3 anti-BRIL Fab Light chain (chains L)
MGWSCIILFLVATATGVHSSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKP
GKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFG
QGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (R), FASTA

>8XVK_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
A1D5J	Ambrisentan	C22 H22 N2 O4	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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