6VTL: Acid-sensing ion channel 1

Structure of an acid-sensing ion channel solubilized by styrene maleic acid and in a resting state at high pH. Determined by electron microscopy at 3.65 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 3.65 Å
Organism: Gallus gallus
Chains: 3
Atoms: 10,242
Mol. weight: 181.57 kDa
Ligands: NAG
Released: 11 Mar 2020

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

Secondary structure: helices and β-sheets

6VTL contains 89 α-helices and 63 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.

Chains A and C: 30 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	31-34	4
α-helix	42-52	11
α-helix	56-70	15
β-strand	74-82	9	1
β-strand	86-87	2	2
α-helix	88-89	2
β-strand	90-95	6	3
α-helix	108-111	4
α-helix	133-140	8
α-helix	155-161	7
α-helix	166-169	4
β-strand	174-175	2	4
β-strand	178-179	2	4
α-helix	182-184	3
β-strand	186-190	5	3
β-strand	193-197	5	3
α-helix	205-208	4
β-strand	209-210	2	2
β-strand	219	1	4
β-strand	221-224	4	1
α-helix	227-229	3
α-helix	231-233	3
β-strand	244	1	5
β-strand	246-251	6	3
α-helix	256-257	2
α-helix	259-262	4
β-strand	264-266	3	3
β-strand	270-282	13	1
β-strand	292	1	6
α-helix	306-322	17
β-strand	325	1	7
α-helix	333-334	2
β-strand	335	1	7
α-helix	336-337	2
α-helix	338-340	3
α-helix	341-345	5
α-helix	346-350	5
α-helix	351-355	5
α-helix	357-359	3
α-helix	363-364	2
β-strand	365	1	6
β-strand	367-379	13	1
α-helix	383-385	3
α-helix	386-391	6
α-helix	397-403	7
β-strand	404-411	8	1
β-strand	415-423	9	1
α-helix	427-431	5
α-helix	435-441	7
α-helix	446-459	14

Chain B: 29 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	31-34	4
α-helix	42-52	11
α-helix	56-70	15
β-strand	74-82	9	11
β-strand	86-87	2	14
α-helix	88-89	2
β-strand	90-95	6	15
α-helix	108-111	4
α-helix	133-140	8
α-helix	155-161	7
α-helix	166-169	4
β-strand	174-175	2	16
β-strand	178-179	2	16
α-helix	182-184	3
β-strand	186-190	5	15
β-strand	193-197	5	15
α-helix	205-208	4
β-strand	209-210	2	14
β-strand	219	1	16
β-strand	221-224	4	11
α-helix	227-229	3
α-helix	231-233	3
β-strand	244	1	1
β-strand	246-251	6	15
α-helix	256-257	2
α-helix	259-262	4
β-strand	264-266	3	15
β-strand	270-282	13	11
β-strand	292	1	17
α-helix	306-322	17
β-strand	325	1	18
α-helix	333-334	2
β-strand	335	1	18
α-helix	336-337	2
α-helix	338-340	3
α-helix	341-345	5
α-helix	346-350	5
α-helix	351-355	5
α-helix	357-359	3
β-strand	365	1	17
β-strand	367-379	13	11
α-helix	383-385	3
α-helix	386-391	6
α-helix	397-403	7
β-strand	404-411	8	11
β-strand	415-423	9	11
α-helix	427-431	5
α-helix	435-441	7
α-helix	446-459	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acid-sensing ion channel 1	A, B, C	protein	527	Gallus gallus	Q1XA76 (AlphaFold model)

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

>6VTL_1 Acid-sensing ion channel 1 (chains A, B, C)
MMDLKVDEEEVDSGQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLAL
VCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLN
NRYEIPDTQTADEKQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQC
SPEDFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDET
SFEAGIKVQIHSQDEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEF
YDTYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYC
VCEMPCNVTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIE
QKKAYEVAGLLGDIGGQMGLFIGASILTVLELFDYAYEVIKHRLCRRGKCRKNHKRNNTD
KGVALSMDDVKRHNPCESLRGHPAGMTYAANILPHHPARGTFEDFTC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

The His-Gly motif of acid-sensing ion channels resides in a reentrant 'loop' implicated in gating and ion selectivity. Yoder, N., Gouaux, E. Elife (2020) 9. DOI 10.7554/eLife.56527 · 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
6X9H 3.01 Å, Molecular mechanism and structural basis of small-molecule modulation of acid-sensing…

Browse structure collections

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