5Y31: Human LGI1-ADAM22 complex

Crystal structure of human LGI1-ADAM22 complex. Determined by X-ray diffraction at 7.13 Å resolution. Released 2 May 2018.

Method: X-ray diffraction
Resolution: 7.13 Å
Organism: Homo sapiens
Chains: 4
Atoms: 15,832
Mol. weight: 237.28 kDa
Ligands: CA, NAG
Released: 2 May 2018

Explore 5Y31 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y31 contains 60 α-helices and 170 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 A: 22 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	238	1
β-strand	239-247	9	1
α-helix	249-254	6
α-helix	259-280	22
β-strand	283-292	10	1
α-helix	300-302	3
α-helix	305-318	14
β-strand	326-331	6	1
β-strand	341-343	3	1
β-strand	355-359	5	1
α-helix	363-378	16
α-helix	384-389	6
β-strand	401	1	2
α-helix	405-406	2
β-strand	413	1	2
α-helix	416-427	12
α-helix	432-434	3
α-helix	436-438	3
α-helix	463-466	4
β-strand	474	1	3
β-strand	479	1	3
β-strand	491-492	2	4
β-strand	495-496	2	4
α-helix	497-498	2
β-strand	502-504	3	5
β-strand	511	1	6
β-strand	514-515	2	5
α-helix	523-525	3
β-strand	528	1	6
β-strand	529	1	7
α-helix	530	1
β-strand	534-535	2	8
β-strand	540-543	4	8
β-strand	546-548	3	8
α-helix	550-558	9
β-strand	563-564	2	9
α-helix	565-566	2
α-helix	567-576	10
β-strand	578	1	10
β-strand	581	1	10
β-strand	585	1	11
β-strand	590	1	11
α-helix	591-594	4
β-strand	602	1	12
β-strand	605-606	2	9
β-strand	616-617	2	12
β-strand	622-624	3	9
β-strand	635-637	3	9
β-strand	640-641	2	12
β-strand	647-648	2	12
β-strand	650	1	12
α-helix	651-652	2
β-strand	656-658	3	13
β-strand	661-663	3	13
β-strand	668-670	3	13
α-helix	671-674	4
α-helix	687-690	4
β-strand	692-694	3	14
β-strand	695	1	7
β-strand	700-702	3	14
β-strand	706-707	2	15
β-strand	713-714	2	15

Chain B: 8 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	46-48	3	16
β-strand	52-56	5	16
β-strand	71-75	5	16
β-strand	81-82	2	17
β-strand	95-99	5	16
β-strand	102-103	2	18
β-strand	105-106	2	17
β-strand	119-123	5	16
β-strand	126-127	2	18
β-strand	130	1	17
β-strand	143-145	3	16
β-strand	167-169	3	16
β-strand	176	1	19
α-helix	179-181	3
α-helix	182-190	9
β-strand	194-195	2	16
β-strand	199	1	20
β-strand	202	1	19
α-helix	204-206	3
β-strand	210	1	20
α-helix	211-213	3
α-helix	216-218	3
β-strand	226-232	7	21
β-strand	239-244	6	22
β-strand	247-253	7	22
β-strand	259-265	7	22
β-strand	272-279	8	22
β-strand	283-291	9	23
β-strand	294-301	8	23
β-strand	307-312	6	23
β-strand	317-323	7	23
β-strand	332-340	9	24
β-strand	343-350	8	24
α-helix	356	1
β-strand	357-362	6	24
β-strand	367-373	7	24
β-strand	379-387	9	25
α-helix	388-389	2
β-strand	396-403	8	25
β-strand	409-414	6	25
β-strand	419-425	7	25
β-strand	434-440	7	26
β-strand	443-449	7	26
β-strand	452-461	10	26
β-strand	464-474	11	26
β-strand	479-484	6	27
β-strand	487-492	6	27
α-helix	498	1
β-strand	499-505	7	27
β-strand	510-517	8	27
β-strand	522-530	9	21
β-strand	533-540	8	21
β-strand	545-550	6	21

Chain C: 22 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	238	1
β-strand	239-247	9	28
α-helix	249-254	6
α-helix	259-280	22
β-strand	283-292	10	28
α-helix	300-302	3
α-helix	305-318	14
β-strand	326-331	6	28
β-strand	341-343	3	28
β-strand	355-359	5	28
α-helix	363-378	16
α-helix	384-389	6
β-strand	401	1	29
α-helix	405-406	2
β-strand	413	1	29
α-helix	416-427	12
α-helix	432-434	3
α-helix	436-438	3
α-helix	463-466	4
β-strand	474	1	30
β-strand	479	1	30
β-strand	491-492	2	31
β-strand	495-496	2	31
α-helix	497-498	2
β-strand	502-504	3	32
β-strand	511	1	33
β-strand	514-515	2	32
α-helix	523-525	3
β-strand	528	1	33
β-strand	529	1	34
α-helix	530	1
β-strand	534-535	2	35
β-strand	540-543	4	35
β-strand	546-548	3	35
α-helix	550-558	9
β-strand	563-564	2	36
α-helix	565-566	2
α-helix	567-576	10
β-strand	578	1	37
β-strand	581	1	37
β-strand	585-586	2	38
β-strand	589-590	2	38
α-helix	591-594	4
β-strand	602	1	39
β-strand	605-606	2	36
β-strand	616-617	2	39
β-strand	622-624	3	36
β-strand	635-637	3	36
β-strand	640-641	2	39
β-strand	647-648	2	39
β-strand	650	1	39
α-helix	651-652	2
β-strand	656-658	3	40
β-strand	661-663	3	40
β-strand	668-670	3	40
α-helix	671-674	4
α-helix	688-690	3
β-strand	692-694	3	41
β-strand	695	1	34
β-strand	700-702	3	41
β-strand	706-707	2	42
β-strand	713-714	2	42

Chain D: 8 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	46-48	3	43
β-strand	52-56	5	43
β-strand	71-75	5	43
β-strand	81-82	2	44
β-strand	95-99	5	43
β-strand	102-103	2	45
β-strand	105-106	2	44
β-strand	119-123	5	43
β-strand	126-127	2	45
β-strand	130	1	44
β-strand	143-145	3	43
β-strand	167-169	3	43
β-strand	176	1	46
α-helix	179-181	3
α-helix	182-190	9
β-strand	194-195	2	43
β-strand	199	1	47
β-strand	202	1	46
α-helix	204-206	3
β-strand	210	1	47
α-helix	211-213	3
α-helix	216-218	3
β-strand	226-232	7	48
β-strand	239-244	6	49
β-strand	247-253	7	49
β-strand	259-265	7	49
β-strand	272-279	8	49
β-strand	283-291	9	50
β-strand	294-301	8	50
β-strand	307-312	6	50
β-strand	317-323	7	50
β-strand	332-340	9	51
β-strand	343-350	8	51
α-helix	356	1
β-strand	357-362	6	51
β-strand	367-373	7	51
β-strand	379-387	9	52
α-helix	388-389	2
β-strand	396-403	8	52
β-strand	409-414	6	52
β-strand	419-425	7	52
β-strand	434-440	7	53
β-strand	443-449	7	53
β-strand	454-461	8	53
β-strand	464-472	9	53
β-strand	479-484	6	54
β-strand	487-492	6	54
α-helix	498	1
β-strand	499-505	7	54
β-strand	510-517	8	54
β-strand	522-530	9	48
β-strand	533-540	8	48
β-strand	545-550	6	48

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Disintegrin and metalloproteinase domain-containing protein 22	A, C	protein	497	Homo sapiens	Q9P0K1 (AlphaFold model)
Leucine-rich glioma-inactivated protein 1	B, D	protein	544	Homo sapiens	O95970 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5Y31_1 Disintegrin and metalloproteinase domain-containing protein 22 (chains A, C)
NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMET
WATDNKFAISENPLITLREFMKYRRDFIKEKSDAVHLFSGSQFESSRSGAAYIGGICSLL
KGGGVNEFGKTDLMAVTLAQSLAHNIGIISDKRKLASGECKCEDTWSGCIMGDTGYYLPK
KFTQCNIEEYHDFLNSGGGACLFNKPSKLLDPPECGNGFIETGEECDCGTPAECVLEGAE
CCKKCTLTQDSQCSDGLCCKKCKFQPMGTVCREAVNDCDIRETCSGNSSQCAPNIHKMDG
YSCDGVQGICFGGRCKTRDRQCKYIWGQKVTASDKYCYEKLNIEGTEKGNCGKDKDTWIQ
CNKRDVLCGYLLCTNIGNIPRLGELDGEITSTLVVQQGRTLNCSGGHVKLEEDVDLGYVE
DGTPCGPQMMCLEHRCLPVASFNFSTCLSSKEGTICSGNGVCSNELKCVCNRHWIGSDCN
TYFPHNDDAKTGITLSG

Sequence of entity 2 (B, D), FASTA

>5Y31_2 Leucine-rich glioma-inactivated protein 1 (chains B, D)
DAAQPARRARRTYEAYPAKPKCPAVCTCTKDNALCENARSIPRTVPPDVISLSFVRSGFT
EISEGSFLFTPSLQLLLFTSNSFDVISDDAFIGLPHLEYLFIENNNIKSISRHTFRGLKS
LIHLSLANNNLQTLPKDIFKGLDSLTNVDLRGNSFNCDCKLKWLVEWLGHTNATVEDIYC
EGPPEYKKRKINSLSSKDFDCIITEFAKSQDLPYQSLSIDTFSYLNDEYVVIAQPFTGKC
IFLEWDHVEKTFRNYDNITGTSTVVCKPIVIETQLYVIVAQLFGGSHIYKRDSFANKFIK
IQDIEILKIRKPNDIETFKIENNWYFVVADSSKAGFTTIYKWNGNGFYSHQSLHAWYRDT
DVEYLEIVRTPQTLRTPHLILSSSSQRPVIYQWNKATQLFTNQTDIPNMEDVYAVKHFSV
KGDVYICLTRFIGDSKVMKWGGSSFQDIQAMPSRGSMVFQPLQINNYQYAILGSDYSFTQ
VYNWDAEKAKFVKFQELNVQAPRSFTHVSINKRNFLFASSFKGNTQIYKHVIVDLSAKHH
HHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22. Yamagata, A., Miyazaki, Y., Yokoi, N. et al. Nat Commun (2018) 9:1546-1546. DOI 10.1038/s41467-018-03947-w · PubMed

Other PDB entries of the same protein (UniProt Q9P0K1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CQF 1.8 Å, Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide
3G5C 2.36 Å, Structural and biochemical studies on the ectodomain of human ADAM22
5Y2Z 2.67 Å, Crystal structure of human LGI1 EPTP-ADAM22 complex
9KZC 2.78 Å, Cryo-EM structure of the LGI1 LRR-LGI1 EPTP-ADAM22 ECD complex
8HQ2 2.93 Å, Crystal structure of human ADAM22 in complex with human LGI1 mutant
8Y6B 3.49 Å, Structure of human LGI1-ADAM22 complex in space group P212121
9KZT 3.79 Å, Cryo-EM structure of the 3:3 LGI1-ADAM22 complex
8HQ1 4.17 Å, Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2
8HPY 5.87 Å, Crystal structure of human LGI1-ADAM22 complex

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