5Y2Z: Human LGI1 EPTP-ADAM22 complex

Crystal structure of human LGI1 EPTP-ADAM22 complex. Determined by X-ray diffraction at 2.67 Å resolution. Released 2 May 2018.

Method: X-ray diffraction
Resolution: 2.67 Å
Organism: Homo sapiens
Chains: 12
Atoms: 39,417
Mol. weight: 583.49 kDa
Ligands: NAG, CA
Released: 2 May 2018

Explore 5Y2Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y2Z contains 144 α-helices and 404 β-strands across 12 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: 21 helices, 42 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	363-377	15
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
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	531	1	8
β-strand	533	1	8
β-strand	534-535	2	9
β-strand	540-543	4	9
β-strand	546-548	3	9
α-helix	550-558	9
β-strand	563-564	2	10
α-helix	565-566	2
α-helix	567-576	10
β-strand	578	1	11
β-strand	581	1	11
β-strand	585-586	2	12
β-strand	589-590	2	12
α-helix	591-594	4
β-strand	602	1	13
β-strand	605-606	2	10
β-strand	616-617	2	13
β-strand	622-624	3	10
β-strand	635-637	3	10
β-strand	640-641	2	13
β-strand	647-648	2	13
β-strand	650	1	13
α-helix	651-652	2
β-strand	656-658	3	14
β-strand	661-663	3	14
β-strand	668-670	3	14
α-helix	671-674	4
α-helix	687-690	4
β-strand	692-694	3	15
β-strand	695	1	7
β-strand	700-702	3	15
β-strand	706-707	2	16
β-strand	713-714	2	16

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	226-232	7	89
β-strand	239-244	6	90
β-strand	247-253	7	90
β-strand	259-266	8	90
β-strand	271-279	9	90
β-strand	283-291	9	91
β-strand	294-301	8	91
β-strand	307-312	6	91
β-strand	317-323	7	91
β-strand	332-340	9	92
β-strand	343-350	8	92
α-helix	356	1
β-strand	357-362	6	92
β-strand	367-373	7	92
β-strand	379-387	9	93
α-helix	388-389	2
β-strand	396-403	8	93
β-strand	409-414	6	93
β-strand	419-425	7	93
β-strand	434-440	7	94
β-strand	443-449	7	94
β-strand	452-461	10	94
β-strand	464-474	11	94
β-strand	479-484	6	95
β-strand	487-492	6	95
α-helix	498	1
β-strand	499-505	7	95
β-strand	510-517	8	95
β-strand	522-530	9	89
β-strand	533-540	8	89
β-strand	545-550	6	89

Chain C: 22 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	238	1
β-strand	239-247	9	17
α-helix	249-254	6
α-helix	259-280	22
β-strand	283-292	10	17
α-helix	300-302	3
α-helix	305-319	15
β-strand	326-331	6	17
β-strand	341-343	3	17
β-strand	355-359	5	17
α-helix	363-378	16
α-helix	384-389	6
α-helix	405-406	2
α-helix	416-427	12
α-helix	432-434	3
α-helix	437-438	2
α-helix	463-468	6
β-strand	474	1	18
β-strand	479	1	18
β-strand	491-492	2	19
β-strand	495-496	2	19
α-helix	497-498	2
β-strand	502-504	3	20
β-strand	511	1	21
β-strand	514-515	2	20
α-helix	523-525	3
β-strand	528	1	21
β-strand	529	1	22
α-helix	530	1
β-strand	531	1	23
β-strand	533	1	23
β-strand	534-535	2	24
β-strand	540-543	4	24
β-strand	546-548	3	24
α-helix	550-558	9
β-strand	563-564	2	25
α-helix	565-566	2
α-helix	567-573	7
β-strand	578	1	26
β-strand	581	1	26
α-helix	598-600	3
β-strand	602	1	27
β-strand	605-606	2	25
β-strand	616-617	2	27
β-strand	622-625	4	25
β-strand	634-637	4	25
β-strand	640-641	2	27
β-strand	647-648	2	27
β-strand	650	1	27
α-helix	651-652	2
β-strand	656-658	3	28
β-strand	661-663	3	28
β-strand	668-670	3	28
α-helix	671-674	4
α-helix	687-690	4
β-strand	692-694	3	29
β-strand	695	1	22
β-strand	700-702	3	29
β-strand	706-707	2	30
β-strand	713-714	2	30

Chain D: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	226-232	7	96
β-strand	239-244	6	97
β-strand	247-253	7	97
β-strand	259-266	8	97
β-strand	271-279	9	97
β-strand	283-291	9	98
β-strand	294-301	8	98
β-strand	307-312	6	98
β-strand	317-323	7	98
β-strand	332-340	9	99
β-strand	343-350	8	99
α-helix	356	1
β-strand	357-362	6	99
β-strand	367-373	7	99
β-strand	379-387	9	100
α-helix	388-389	2
β-strand	396-403	8	100
β-strand	409-414	6	100
β-strand	419-425	7	100
β-strand	434-440	7	101
β-strand	443-449	7	101
β-strand	452-460	9	101
β-strand	465-474	10	101
β-strand	479-484	6	102
β-strand	487-492	6	102
α-helix	498	1
β-strand	499-505	7	102
β-strand	510-517	8	102
β-strand	522-530	9	96
β-strand	533-540	8	96
β-strand	545-550	6	96

Chain E: 21 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	238	1
β-strand	239-247	9	31
α-helix	249-254	6
α-helix	259-280	22
β-strand	283-292	10	31
α-helix	300-302	3
α-helix	305-318	14
β-strand	326-331	6	31
β-strand	341-343	3	31
β-strand	355-359	5	31
α-helix	363-378	16
α-helix	384-389	6
α-helix	405-406	2
α-helix	416-427	12
α-helix	432-434	3
α-helix	436-438	3
α-helix	463-466	4
β-strand	474-475	2	32
β-strand	478-479	2	32
β-strand	491-492	2	33
β-strand	495-496	2	33
α-helix	497-498	2
β-strand	502-504	3	34
β-strand	511	1	35
β-strand	514-515	2	34
α-helix	523-525	3
β-strand	528	1	35
β-strand	529	1	36
α-helix	530	1
β-strand	534-535	2	37
β-strand	540-543	4	37
β-strand	546-548	3	37
α-helix	550-558	9
β-strand	563-564	2	38
α-helix	565-566	2
α-helix	567-573	7
β-strand	578	1	39
β-strand	581	1	39
β-strand	602	1	40
β-strand	605-606	2	38
β-strand	616-617	2	40
β-strand	622	1	41
β-strand	636	1	38
β-strand	637	1	41
β-strand	640-641	2	40
β-strand	647-648	2	40
β-strand	650	1	40
α-helix	651-652	2
β-strand	656-658	3	42
β-strand	661-663	3	42
β-strand	668-670	3	42
α-helix	671-674	4
α-helix	687-690	4
β-strand	692-694	3	43
β-strand	695	1	36
β-strand	700-702	3	43
β-strand	706-707	2	44
β-strand	713-714	2	44

Chain F: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	226-232	7	103
β-strand	239-244	6	104
β-strand	247-253	7	104
β-strand	259	1	105
β-strand	260-265	6	104
β-strand	272-276	5	104
β-strand	279	1	105
β-strand	283-291	9	106
β-strand	294-301	8	106
β-strand	307-312	6	106
β-strand	317-323	7	106
β-strand	332-340	9	107
β-strand	343-350	8	107
α-helix	356	1
β-strand	357-362	6	107
β-strand	367-373	7	107
β-strand	379-387	9	108
α-helix	388-389	2
β-strand	396-403	8	108
β-strand	409-414	6	108
β-strand	419-425	7	108
β-strand	434-440	7	109
β-strand	443-449	7	109
β-strand	452-460	9	109
β-strand	465-474	10	109
β-strand	479-484	6	110
β-strand	487-492	6	110
α-helix	498	1
β-strand	499-505	7	110
β-strand	510-517	8	110
β-strand	522-530	9	103
β-strand	533-540	8	103
β-strand	545-550	6	103

Chain G: 21 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	238	1
β-strand	239-247	9	45
α-helix	249-254	6
α-helix	259-280	22
β-strand	283-292	10	45
α-helix	300-302	3
α-helix	305-318	14
β-strand	326-331	6	45
β-strand	341-343	3	45
β-strand	355-359	5	45
α-helix	363-378	16
α-helix	384-389	6
β-strand	401	1	46
β-strand	413	1	46
α-helix	416-427	12
α-helix	432-434	3
α-helix	436-438	3
α-helix	463-466	4
β-strand	474	1	47
β-strand	479	1	47
β-strand	491-492	2	48
β-strand	495-496	2	48
α-helix	497-498	2
β-strand	502-504	3	49
β-strand	511	1	50
β-strand	514-515	2	49
α-helix	523-525	3
β-strand	528	1	50
β-strand	529	1	51
α-helix	530	1
β-strand	534-535	2	52
β-strand	540-543	4	52
β-strand	546-548	3	52
α-helix	550-558	9
β-strand	563-564	2	53
α-helix	565-566	2
α-helix	567-573	7
α-helix	597-600	4
β-strand	602	1	54
β-strand	605-606	2	53
β-strand	616-617	2	54
β-strand	636	1	53
β-strand	640-641	2	54
β-strand	647-648	2	54
β-strand	650	1	54
α-helix	651-652	2
β-strand	656-658	3	55
β-strand	661-663	3	55
β-strand	668-670	3	55
α-helix	671-674	4
α-helix	687-690	4
β-strand	692-694	3	56
β-strand	695	1	51
β-strand	700-702	3	56
β-strand	706-707	2	57
β-strand	713-714	2	57

Chain H: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	225-232	8	111
β-strand	239-244	6	112
β-strand	247-253	7	112
β-strand	259-266	8	112
β-strand	271-279	9	112
β-strand	283-291	9	113
β-strand	294-301	8	113
β-strand	307-312	6	113
β-strand	317-323	7	113
β-strand	332-340	9	114
β-strand	343-350	8	114
α-helix	356	1
β-strand	357-362	6	114
β-strand	367-373	7	114
β-strand	379-387	9	115
α-helix	388-389	2
β-strand	396-403	8	115
β-strand	409-414	6	115
β-strand	419-425	7	115
β-strand	434-440	7	116
β-strand	443-449	7	116
β-strand	452-460	9	116
β-strand	465-474	10	116
β-strand	479-484	6	117
β-strand	487-492	6	117
α-helix	498	1
β-strand	499-505	7	117
β-strand	510-517	8	117
β-strand	522-530	9	111
β-strand	533-540	8	111
β-strand	545-551	7	111

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Disintegrin and metalloproteinase domain-containing protein 22	A, C, E, G, I, K	protein	504	Homo sapiens	Q9P0K1 (AlphaFold model)
Leucine-rich glioma-inactivated protein 1	B, D, F, H, J, L	protein	347	Homo sapiens	O95970 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>5Y2Z_1 Disintegrin and metalloproteinase domain-containing protein 22 (chains A, C, E, G, I, K)
NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMET
WATDNKFAISENPLITLREFMKYRRDFIKEKSDAVHLFSGSQFESSRSGAAYIGGICSLL
KGGGVNEFGKTDLMAVTLAQSLAHNIGIISDKRKLASGECKCEDTWSGCIMGDTGYYLPK
KFTQCNIEEYHDFLNSGGGACLFNKPSKLLDPPECGNGFIETGEECDCGTPAECVLEGAE
CCKKCTLTQDSQCSDGLCCKKCKFQPMGTVCREAVNDCDIRETCSGNSSQCAPNIHKMDG
YSCDGVQGICFGGRCKTRDRQCKYIWGQKVTASDKYCYEKLNIEGTEKGNCGKDKDTWIQ
CNKRDVLCGYLLCTNIGNIPRLGELDGEITSTLVVQQGRTLNCSGGHVKLEEDVDLGYVE
DGTPCGPQMMCLEHRCLPVASFNFSTCLSSKEGTICSGNGVCSNELKCVCNRHWIGSDCN
TYFPHNDDAKTGITLSGKHHHHHH

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>5Y2Z_2 Leucine-rich glioma-inactivated protein 1 (chains B, D, F, H, J, L)
DAAQPATEFAKSQDLPYQSLSIDTFSYLNDEYVVIAQPFTGKCIFLEWDHVEKTFRNYDN
ITGTSTVVCKPIVIETQLYVIVAQLFGGSHIYKRDSFANKFIKIQDIEILKIRKPNDIET
FKIENNWYFVVADSSKAGFTTIYKWNGNGFYSHQSLHAWYRDTDVEYLEIVRTPQTLRTP
HLILSSSSQRPVIYQWNKATQLFTNQTDIPNMEDVYAVKHFSVKGDVYICLTRFIGDSKV
MKWGGSSFQDIQRMPSRGSMVFQPLQINNYQYAILGSDYSFTQVYNWDAEKAKFVKFQEL
NVQAPRSFTHVSINKRNFLFASSFKGNTQIYKHVIVDLSAKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	24

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
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
5Y31 7.13 Å, Crystal structure of human LGI1-ADAM22 complex

Browse structure collections

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