7RNN: Human ASIC1a-Nb.C1 complex

Human ASIC1a-Nb.C1 complex. Determined by electron microscopy at 2.86 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 2.86 Å
Organisms: Vicugna pacos, Homo sapiens
Chains: 2
Atoms: 4,000
Mol. weight: 73.21 kDa
Ligands: NAG
Released: 11 Aug 2021

Explore 7RNN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RNN contains 26 α-helices and 31 β-strands across 2 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 C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	1
β-strand	16	1	2
β-strand	22-27	6	1
α-helix	33-35	3
β-strand	38-43	6	3
β-strand	49-55	7	3
β-strand	62-64	3	3
β-strand	72-77	6	1
β-strand	82-87	6	1
α-helix	92-94	3
β-strand	96-102	7	3
β-strand	114-116	3	3
β-strand	118	1	2

Chain D: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	41-70	30
β-strand	73-81	9	4
β-strand	85-86	2	5
α-helix	87-88	2
β-strand	89-94	6	6
α-helix	105-110	6
α-helix	132-139	8
α-helix	149-151	3
α-helix	154-161	8
α-helix	163-164	2
α-helix	165-168	4
β-strand	169-171	3	4
β-strand	173-174	2	4
β-strand	177-178	2	4
α-helix	181-183	3
β-strand	184-189	6	6
β-strand	192-197	6	6
α-helix	204-207	4
β-strand	208-209	2	5
β-strand	218-223	6	4
α-helix	226-228	3
α-helix	230-231	2
β-strand	245-250	6	6
α-helix	255-256	2
α-helix	258-261	4
β-strand	263-265	3	6
β-strand	269-281	13	4
β-strand	291	1	7
α-helix	307-323	17
β-strand	326	1	8
α-helix	335	1
β-strand	336	1	8
α-helix	337-338	2
α-helix	339-342	4
α-helix	347-355	9
α-helix	364-365	2
β-strand	366	1	7
β-strand	368-380	13	4
α-helix	387-393	7
α-helix	398-404	7
β-strand	405-412	8	4
β-strand	416-424	9	4
α-helix	428-442	15
α-helix	447-461	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobodies Nb.C1	C	protein	116	Vicugna pacos
Acid-sensing ion channel 1	D	protein	528	Homo sapiens	P78348 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7RNN_1 Nanobodies Nb.C1 (chains C)
QVQLVESGGGLVQPRGSLRLSCAASGFTFSRAAMSWYRQAPGKEREMVSTIGSFGVSTNY
SDSVKGRFTISRDNAKNTVYLHMNSLKPEDTAVYYCNARYRSSYPWGQGTQVTVSS

Sequence of entity 2 (D), FASTA

>7RNN_2 Acid-sensing ion channel 1 (chains D)
MELKAEEEEVGGVQPVSIQAFASSSTLHGLAHIFSYERLSLKRALWALCFLGSLAVLLCV
CTERVQYYFHYHHVTKLDEVAASQLTFPAVTFCNLNEFRFSQVSKNDLYHAGELLALLNN
RYEIPDTQMADEKQLEILQDKANFRSFKPKPFNMREFYDRAGHDIRDMLLSCHFRGEVCS
AEDFKVVFTRYGKCYTFNSGRDGRPRLKTMKGGTGNGLEIMLDIQQDEYLPVWGETDETS
FEAGIKVQIHSQDEPPFIDQLGFGVAPGFQTFVACQEQRLIYLPPPWGTCKAVTMDSDLD
FFDSYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDQEY
CVCEMPCNLTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEVLNYETI
EQKKAYEIAGLLGDIGGQMGLFIGASILTVLELFDYAYEVIKHKLCRRGKCQKEAKRSSA
DKGVALSLDDVKRHNPCEGLRGHPAGMTYAANILPHHPARGTFEDFTC

Ligands and cofactors

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

Primary citation

Structure and analysis of nanobody binding to the human ASIC1a ion channel. Wu, Y., Chen, Z., Sigworth, F.J. et al. Elife (2021) 10. DOI 10.7554/eLife.67115 · PubMed

Other PDB entries of the same protein (UniProt P78348 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E4I 2.33 Å, Human ASIC1a at pH 7.5 in complex with MitTx
9E4H 2.61 Å, Human ASIC1a at pH 5.7 with rotated, domain-swapped transmembrane domain
9E4F 2.69 Å, Human ASIC1a at pH 5.7 with domain-swapped transmembrane domain
9E4A 2.74 Å, Human ASIC1a at pH 8.5 with domain-swapped transmembrane domain
9E4K 2.77 Å, Human ASIC1a at pH 8.5, T26V mutation
9E4G 2.8 Å, Human ASIC1a at pH 5.7 with linear transmembrane domain
6L6N 2.86 Å, hASIC1a co-crystallized with Nafamostat
9E4J 2.87 Å, Human ASIC1a at pH 6.5 in complex with MitTx
9E4B 3.09 Å, Human ASIC1a at pH 7.5 with domain-swapped transmembrane domain
9E4E 3.16 Å, Human ASIC1a at pH 6.5 with linear transmembrane domain
9E4D 3.19 Å, Human ASIC1a at pH 7.5 with linear transmembrane domain
6L6I 3.24 Å, hASIC1a co-crystallized with Mamb-1

Browse structure collections

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