6X9H: Acid-sensing ion channel 1

Molecular mechanism and structural basis of small-molecule modulation of acid-sensing ion channel 1 (ASIC1). Determined by X-ray diffraction at 3.01 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 3.01 Å
Organism: Gallus gallus
Chains: 3
Atoms: 9,827
Mol. weight: 152.31 kDa
Ligands: NAG, UZG
Released: 30 Dec 2020

Explore 6X9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X9H contains 71 α-helices and 57 β-strands across 3 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: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	45-70	26
β-strand	74-82	9	1
β-strand	86-87	2	2
β-strand	90-95	6	3
α-helix	101-103	3
α-helix	106-112	7
α-helix	133-142	10
α-helix	155-162	8
α-helix	164-165	2
α-helix	166-169	4
β-strand	170-175	6	1
β-strand	178-179	2	1
α-helix	182-184	3
β-strand	185-190	6	3
β-strand	193-198	6	3
α-helix	205-208	4
β-strand	209-210	2	2
β-strand	219-224	6	1
α-helix	227-229	3
α-helix	231-232	2
β-strand	244	1	4
β-strand	246-251	6	3
α-helix	259-262	4
β-strand	264-266	3	3
β-strand	270-282	13	1
β-strand	292	1	5
α-helix	306-322	17
β-strand	325	1	6
α-helix	333-334	2
β-strand	335	1	6
α-helix	336-337	2
α-helix	338-340	3
α-helix	341-345	5
α-helix	346-352	7
α-helix	363-364	2
β-strand	365	1	5
β-strand	367-379	13	1
α-helix	383-393	11
α-helix	397-403	7
β-strand	404-423	20	1
α-helix	427-441	15
α-helix	446-451	6

Chain B: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	43-70	28
β-strand	74-82	9	4
β-strand	86-87	2	7
β-strand	90-95	6	8
α-helix	101-103	3
α-helix	106-112	7
α-helix	133-142	10
α-helix	155-162	8
α-helix	164-165	2
α-helix	166-169	4
β-strand	170-175	6	4
β-strand	178-179	2	4
α-helix	182-184	3
β-strand	185-190	6	8
β-strand	193-198	6	8
α-helix	205-208	4
β-strand	209-210	2	7
α-helix	215-217	3
β-strand	219-224	6	4
α-helix	227-229	3
α-helix	231-232	2
β-strand	244	1	9
β-strand	246-251	6	8
α-helix	259-262	4
β-strand	264-266	3	8
β-strand	270-282	13	4
β-strand	292	1	10
α-helix	306-322	17
β-strand	325	1	11
α-helix	334	1
β-strand	335	1	11
α-helix	336-337	2
α-helix	338-340	3
α-helix	341-345	5
α-helix	346-353	8
α-helix	363-364	2
β-strand	365	1	10
β-strand	367-379	13	4
α-helix	383-393	11
α-helix	397-403	7
β-strand	404-423	20	4
α-helix	427-441	15
α-helix	446-449	4
α-helix	451-455	5

Chain C: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	51-70	20
β-strand	74-82	9	9
β-strand	86-87	2	12
β-strand	90-95	6	13
α-helix	106-112	7
α-helix	133-142	10
α-helix	155-162	8
α-helix	164-165	2
α-helix	166-169	4
β-strand	170-175	6	9
β-strand	178-179	2	9
α-helix	182-184	3
β-strand	185-190	6	13
β-strand	193-198	6	13
α-helix	205-208	4
β-strand	209-210	2	12
β-strand	219-224	6	9
α-helix	227-229	3
α-helix	231-232	2
β-strand	244	1	1
β-strand	246-251	6	13
α-helix	259-262	4
β-strand	264-266	3	13
β-strand	270-282	13	9
β-strand	292	1	14
α-helix	306-322	17
β-strand	325	1	15
α-helix	334	1
β-strand	335	1	15
α-helix	336-337	2
α-helix	338-340	3
α-helix	341-345	5
α-helix	346-351	6
α-helix	352-356	5
α-helix	363-364	2
β-strand	365	1	14
β-strand	367-379	13	9
α-helix	383-392	10
α-helix	397-403	7
β-strand	404-423	20	9
α-helix	427-441	15
α-helix	446-454	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acid-sensing ion channel 1	A, B, C	protein	438	Gallus gallus	Q1XA76 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6X9H_1 Acid-sensing ion channel 1 (chains A, B, C)
STLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATR
LTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADEKQLEILQDKANF
RNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYGKCYTFNAGQDGK
PRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPLIDQLGFG
VAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDCETRYLVENCNCR
MVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGKELSMVKIPSKAS
AKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGDIGGQMGLFIGAS
ILTVLELFDYAYEVIKHR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
UZG	2-[4-(3,4-dimethoxyphenoxy)phenyl]-1H-benzimidazole-6-carboximidamide	C22 H20 N4 O3	3

Water and common crystallization additives (NA) are not listed.

Primary citation

Molecular mechanism and structural basis of small-molecule modulation of the gating of acid-sensing ion channel 1. Liu, Y., Ma, J., DesJarlais, R.L. et al. Commun Biol (2021) 4:174-174. DOI 10.1038/s42003-021-01678-1 · PubMed

Other PDB entries of the same protein (UniProt Q1XA76 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QTS 1.9 Å, Structure of an acid-sensing ion channel 1 at 1.9 A resolution and low pH
4NTW 2.07 Å, Structure of acid-sensing ion channel in complex with snake toxin
4NTX 2.27 Å, Structure of acid-sensing ion channel in complex with snake toxin and amiloride
3S3W 2.6 Å, Structure of chicken acid-sensing ion channel 1 at 2.6 a resolution and ph 7.5
4NTY 2.65 Å, Cesium sites in the crystal structure of acid-sensing ion channel in complex with snake…
4FZ0 2.8 Å, Crystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at low pH
6VTK 2.82 Å, Structure of an acid-sensing ion channel solubilized by styrene maleic acid and in a…
5WKU 2.95 Å, Structure of an acid sensing ion channel in a resting state with barium
3S3X 2.99 Å, Structure of chicken acid-sensing ion channel 1 AT 3.0 A resolution in complex with…
3IJ4 3.0 Å, Cesium sites in the crystal structure of a functional acid sensing ion channel in the…
4NYK 3.0 Å, Structure of a membrane protein
5WKV 3.2 Å, Structure of an acid sensing ion channel in a resting state with calcium

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