5TJ4: PDB entry 5TJ4

Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Pro306 fused to maltose binding protein. Determined by X-ray diffraction at 3.5 Å resolution. Released 1 Feb 2017.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 10
Atoms: 39,838
Mol. weight: 617.17 kDa
Released: 1 Feb 2017

Explore 5TJ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TJ4 contains 301 α-helices and 256 β-strands across 10 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: 30 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
α-helix	17-31	15
β-strand	34-38	5	1
α-helix	43-53	11
β-strand	59-63	5	1
α-helix	64-66	3
α-helix	67-73	7
β-strand	76	1	2
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	3
α-helix	91-96	6
β-strand	98-99	2	4
β-strand	102-103	2	4
β-strand	106-111	6	1
β-strand	114-118	5	5
β-strand	128	1	6
α-helix	132-141	10
β-strand	145	1	7
α-helix	154-163	10
β-strand	169-172	4	8
β-strand	175-181	7	8
α-helix	186-200	15
α-helix	210-218	9
β-strand	222	1	7
β-strand	224-227	4	5
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	5
α-helix	246-248	3
β-strand	249-250	2	6
β-strand	253-254	2	6
β-strand	258-259	2	9
β-strand	260-266	7	1
β-strand	267	1	2
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	1
β-strand	304	1	3
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	9
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
β-strand	1229	1	10
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1297	16
α-helix	1309-1313	5
β-strand	1315	1	11
β-strand	1321	1	11
α-helix	1323-1338	16
α-helix	1343-1352	10
α-helix	1355-1365	11
α-helix	1385-1402	18

Chain B: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	12
α-helix	17-31	15
β-strand	34-38	5	12
α-helix	43-53	11
β-strand	59-63	5	12
α-helix	64-66	3
α-helix	67-73	7
β-strand	76	1	13
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	14
α-helix	91-96	6
β-strand	98-99	2	15
β-strand	102-103	2	15
β-strand	106-111	6	12
β-strand	114-118	5	16
β-strand	128	1	17
α-helix	132-141	10
β-strand	145-147	3	16
α-helix	154-163	10
β-strand	167-172	6	18
β-strand	175-182	8	18
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	16
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	16
α-helix	246-248	3
β-strand	249-250	2	17
β-strand	253-254	2	17
β-strand	258-259	2	19
β-strand	260-266	7	12
β-strand	267	1	13
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	12
β-strand	304	1	14
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	19
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1298	17
α-helix	1309-1313	5
β-strand	1315	1	20
β-strand	1321	1	20
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1365	11
α-helix	1385-1402	18

Chain C: 30 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	21
α-helix	17-31	15
β-strand	34-38	5	21
α-helix	43-53	11
β-strand	59-63	5	21
α-helix	64-66	3
α-helix	67-73	7
β-strand	76	1	22
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	23
α-helix	91-96	6
β-strand	98-99	2	24
β-strand	102-103	2	24
β-strand	106-111	6	21
β-strand	114-118	5	25
β-strand	128	1	26
α-helix	132-141	10
β-strand	145-147	3	25
α-helix	154-163	10
β-strand	167-172	6	10
β-strand	175-182	8	10
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	25
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	25
α-helix	246-248	3
β-strand	249-250	2	26
β-strand	253-254	2	26
β-strand	258-259	2	27
β-strand	260-266	7	21
β-strand	267	1	22
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	21
β-strand	304	1	23
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	27
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
β-strand	1229	1	8
α-helix	1249-1261	13
α-helix	1265-1276	12
α-helix	1282-1298	17
α-helix	1309-1313	5
β-strand	1315	1	28
β-strand	1321	1	28
α-helix	1323-1338	16
α-helix	1343-1352	10
α-helix	1355-1365	11
α-helix	1384-1403	20

Chain D: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	29
α-helix	17-31	15
β-strand	34-38	5	29
α-helix	43-53	11
β-strand	59-63	5	29
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	30
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	31
α-helix	91-96	6
β-strand	98-99	2	32
β-strand	102-103	2	32
β-strand	106-111	6	29
β-strand	114-118	5	33
β-strand	128	1	34
α-helix	132-141	10
β-strand	145-147	3	33
α-helix	154-163	10
β-strand	167-172	6	35
β-strand	175-182	8	35
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	33
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	33
α-helix	246-248	3
β-strand	249-250	2	34
β-strand	253-254	2	34
β-strand	258-259	2	36
β-strand	260-266	7	29
β-strand	267	1	30
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	29
β-strand	304	1	31
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	36
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1298	17
α-helix	1310-1314	5
β-strand	1315	1	37
β-strand	1321	1	37
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1367	13
α-helix	1384-1403	20

Chain E: 30 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	38
α-helix	17-31	15
β-strand	34-38	5	38
α-helix	43-53	11
β-strand	59-63	5	38
α-helix	64-66	3
α-helix	67-73	7
β-strand	76	1	39
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	40
α-helix	91-96	6
β-strand	98-99	2	41
β-strand	102-103	2	41
β-strand	106-111	6	38
β-strand	114-118	5	42
β-strand	128	1	43
α-helix	132-141	10
β-strand	145	1	44
α-helix	154-163	10
β-strand	167-172	6	45
β-strand	175-182	8	45
α-helix	186-200	15
α-helix	210-218	9
β-strand	222	1	44
β-strand	224-227	4	42
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	42
α-helix	246-248	3
β-strand	249-250	2	43
β-strand	253-254	2	43
β-strand	258-259	2	46
β-strand	260-266	7	38
β-strand	267	1	39
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	38
β-strand	304	1	40
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	46
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
β-strand	1240	1	47
β-strand	1242	1	47
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1298	17
α-helix	1309-1313	5
β-strand	1315	1	48
β-strand	1321	1	48
α-helix	1323-1338	16
α-helix	1343-1352	10
α-helix	1355-1364	10
α-helix	1384-1402	19

Chain F: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	49
α-helix	17-31	15
β-strand	34-38	5	49
α-helix	43-53	11
β-strand	59-63	5	49
α-helix	64-66	3
α-helix	67-73	7
β-strand	76	1	50
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	51
α-helix	91-96	6
β-strand	98-99	2	52
β-strand	102-103	2	52
β-strand	106-111	6	49
β-strand	114-118	5	53
β-strand	128	1	54
α-helix	132-141	10
β-strand	145-147	3	53
α-helix	154-163	10
β-strand	167-172	6	55
β-strand	175-182	8	55
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	53
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	53
α-helix	246-248	3
β-strand	249-250	2	54
β-strand	253-254	2	54
β-strand	258-259	2	56
β-strand	260-266	7	49
β-strand	267	1	50
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	49
β-strand	304	1	51
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	56
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1298	17
α-helix	1309-1313	5
β-strand	1315	1	57
β-strand	1321	1	57
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1364	10
α-helix	1384-1403	20

Chain G: 31 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	58
α-helix	17-31	15
β-strand	34-38	5	58
α-helix	43-53	11
β-strand	59-63	5	58
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	59
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	60
α-helix	91-96	6
β-strand	98-99	2	61
β-strand	102-103	2	61
β-strand	106-111	6	58
β-strand	114-118	5	62
β-strand	128	1	63
α-helix	132-141	10
β-strand	145-147	3	62
α-helix	154-163	10
β-strand	167-172	6	64
β-strand	175-182	8	64
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	62
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	62
α-helix	246-248	3
β-strand	249-250	2	63
β-strand	253-254	2	63
β-strand	258-259	2	65
β-strand	260-266	7	58
β-strand	267	1	59
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	58
β-strand	304	1	60
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	65
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1298	17
α-helix	1309-1313	5
β-strand	1315	1	66
β-strand	1321	1	66
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1365	11
α-helix	1370-1373	4
α-helix	1384-1403	20

Chain H: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	67
α-helix	17-31	15
β-strand	34-38	5	67
α-helix	43-53	11
β-strand	59-63	5	67
α-helix	64-66	3
α-helix	67-73	7
β-strand	76	1	68
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	69
α-helix	91-96	6
β-strand	98-99	2	70
β-strand	102-103	2	70
β-strand	106-111	6	67
β-strand	114-118	5	71
β-strand	128	1	72
α-helix	132-141	10
β-strand	145-147	3	71
α-helix	154-163	10
β-strand	167-172	6	73
β-strand	175-182	8	73
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	71
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	71
α-helix	246-248	3
β-strand	249-250	2	72
β-strand	253-254	2	72
β-strand	258-259	2	74
β-strand	260-266	7	67
β-strand	267	1	68
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	67
β-strand	304	1	69
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	74
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-1223	18
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1297	16
α-helix	1309-1313	5
β-strand	1315	1	75
β-strand	1321	1	75
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1364	10
α-helix	1384-1403	20

2 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
Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein	A, B, C, D, E, F, G, H, I, J	protein	561	Escherichia coli, Homo sapiens	Q8TAX9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>5TJ4_1 Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein (chains A, B, C, D, E, F, G, H, I, J)
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAA
LAAAQTNAAAMSAGLDIHFRGKTKSFPEGKSLGSEDSRNMKEKLEDMESVLKDLTEEKRK
DVLNSLAKCLGKEDIRQDLEQRVSEVLISGELHMEDPDKPLLSSLFNAAGVLVEARAKAI
LDFLDALLELSEEQQFVAEALEKGTLPLLKDQVKSVMEQNWDELASSPPDMDYDPEARIL
CALYVVVSILLELAEGPTSVS

Primary citation

Gene polymorphism linked to increased asthma and IBD risk alters gasdermin-B structure, a sulfatide and phosphoinositide binding protein. Chao, K.L., Kulakova, L., Herzberg, O. Proc Natl Acad Sci U S A (2017) 114:E1128-E1137. DOI 10.1073/pnas.1616783114 · PubMed

Other PDB entries of the same protein (UniProt Q8TAX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5TIB 2.6 Å, Gasdermin-B C-terminal domain containing the polymorphism residues Arg299:Ser306 fused…
9K1S 2.69 Å, Crystal structure of human granzyme A in complex with GSDMB-C domain
7WJQ 2.7 Å, Crystal structure of GSDMB in complex with Ipah7.8
8GTJ 2.7 Å, Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex
5TJ2 2.8 Å, Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Ser306 fused…
8GTK 3.1 Å, Crystal structure of IpaH7.8-LRR and GSDMB isoform-1 complex
8GTN 3.17 Å, Cryo-EM structure of the gasdermin B pore
9XSG 3.4 Å, CryoEM structure of hGZMA-hGSDMB
21AM 3.59 Å, CryoEM structure of hGZMA-hGSDMBctd
8EFP 3.8 Å, CryoEM structure of GSDMB in complex with shigella IpaH7.8
8ET1 4.48 Å, CryoEM structure of GSDMB pore without transmembrane beta-barrel
8ET2 4.96 Å, CryoEM structure of the GSDMB pore

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