8IF3: Human alpha-2/delta-1 with mirogabalin

Structure of human alpha-2/delta-1 with mirogabalin. Determined by electron microscopy at 3.23 Å resolution. Released 5 Apr 2023.

Method: Electron microscopy
Resolution: 3.23 Å
Organism: Homo sapiens
Chains: 1
Atoms: 7,528
Mol. weight: 127.02 kDa
Ligands: NAG, 8X9
Released: 5 Apr 2023

Explore 8IF3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IF3 contains 33 α-helices and 52 β-strands across 1 chain. 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: 33 helices, 52 β-strands

Element	Residues	Length	Sheet
α-helix	30-52	23
α-helix	54-64	11
β-strand	68-72	5	1
α-helix	75-109	35
β-strand	125-126	2	2
β-strand	150-152	3	3
β-strand	155-159	5	3
β-strand	165-167	3	2
α-helix	173	1
α-helix	177-186	10
α-helix	187-189	3
α-helix	190-199	10
β-strand	205-210	6	2
β-strand	215-217	3	2
α-helix	242-248	7
β-strand	253	1	4
β-strand	254-259	6	5
α-helix	262-264	3
α-helix	267-282	16
β-strand	288	1	4
β-strand	289	1	6
β-strand	291-294	4	5
β-strand	298-300	3	5
β-strand	308	1	6
α-helix	312-323	12
α-helix	333-344	12
β-strand	357-362	6	5
β-strand	384-388	5	5
β-strand	389	1	7
α-helix	397-405	9
β-strand	413	1	7
α-helix	426-430	5
α-helix	432-437	6
β-strand	450-451	2	2
β-strand	458-461	4	2
β-strand	464-466	3	2
β-strand	486-493	8	2
α-helix	494-499	6
β-strand	511-515	5	8
β-strand	520	1	9
β-strand	521-523	3	8
β-strand	541	1	9
α-helix	542-545	4
α-helix	550-558	9
β-strand	565-574	10	8
β-strand	581-592	12	8
β-strand	599-605	7	8
β-strand	610-614	5	1
α-helix	638-640	3
α-helix	641-644	4
β-strand	646-649	4	10
β-strand	655	1	11
α-helix	665-676	12
β-strand	685	1	11
α-helix	687-703	17
α-helix	704-708	5
β-strand	717-724	8	12
β-strand	728-731	4	10
α-helix	734-738	5
α-helix	746-748	3
α-helix	750-757	8
β-strand	761	1	13
β-strand	762-764	3	12
α-helix	765-767	3
β-strand	780-785	6	12
β-strand	788-789	2	14
β-strand	794-795	2	14
β-strand	798-804	7	12
α-helix	806-813	8
β-strand	836-841	6	15
β-strand	846	1	16
β-strand	849-850	2	15
β-strand	862	1	16
α-helix	863-865	3
α-helix	868-877	10
β-strand	880-887	8	17
β-strand	964-971	8	17
β-strand	978-983	6	15
β-strand	988-995	8	15
α-helix	996	1
β-strand	999	1	13
β-strand	1002-1007	6	15
β-strand	1024-1025	2	17
α-helix	1031-1034	4
α-helix	1038-1040	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Voltage-dependent calcium channel subunit alpha-2/delta-1	A	protein	1099	Homo sapiens	P54289 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8IF3_1 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains A)
MAAGCLLALTLTLFQSLLIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVNQLVDI
YEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFASN
EVVYYNAKDDLDPEKNDSEPGSQRIKPVFIEDANFGRQISYQHAAVHIPTDIYEGSTIVL
NELNWTSALDEVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDVRR
RPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQD
VSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKIIML
FTDGGEERAQEIFNKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIR
INTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTNLK
NQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKNPKSQEPVTL
DFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYIDKGNRTYTWTPVNGTDYSL
ALVLPTYSFYYIKAKLEETITQARSKKGKMKDSETLKPDNFEESGYTFIAPRDYCNDLKI
SDNNTEFLLNFNEFIDRHHHHHHHHKTPNNPSCNADLINRVLLDAGFTNELVQNYWSKQK
NIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAPYFNKSG
PGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCDCKRN
SDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDYQSVC
EPGAAPKQGAGHRSAYVPSVADILQIGWWATAAAWSILQQFLLSLTFPRLLEAVEMEDDD
FTASLSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHGEKLMNTNLIFIMVESKGTC
PCDTRLLIQAEQTSDGPNPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSGLNPSLWYI
IGIQFLLLWLVSGSTHRLL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7
8X9	2-[(1R,5S,6S)-6-(aminomethyl)-3-ethyl-6-bicyclo[3.2.0]hept-3-enyl]acetic acid	C12 H19 N O2	1

Primary citation

Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human alpha 2 delta 1, a Voltage-Gated Calcium Channel Subunit. Kozai, D., Numoto, N., Nishikawa, K. et al. J Mol Biol (2023) 435:168049-168049. DOI 10.1016/j.jmb.2023.168049 · PubMed

Other PDB entries of the same protein (UniProt P54289 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VFS 2.8 Å, Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, apo state
8WE6 2.9 Å, Human L-type voltage-gated calcium channel Cav1.2 at 2.9 Angstrom resolution
8WE8 2.9 Å, Human L-type voltage-gated calcium channel Cav1.2 in the presence of calciseptine,…
8X93 2.92 Å, P/Q type calcium channel in complex with omega-Agatoxin IVA
8X90 2.95 Å, P/Q type calcium channel
7MIX 3.0 Å, Human N-type voltage-gated calcium channel Cav2.2 in the presence of ziconotide at 3.0…
7UHG 3.0 Å, Human L-type voltage-gated calcium channel Cav1.3 at 3.0 Angstrom resolution
7VFU 3.0 Å, Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to…
7VFV 3.0 Å, Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to…
7YG5 3.0 Å, Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in…
8WE9 3.0 Å, Human L-type voltage-gated calcium channel Cav1.2 (Class I) in the presence of…
9VLG 3.01 Å, Structure of human alpha-2/delta-1 with crisugabalin

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