5TJ2: PDB entry 5TJ2

Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Ser306 fused to maltose binding protein. Determined by X-ray diffraction at 2.8 Å resolution. Released 1 Feb 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 4
Atoms: 15,875
Mol. weight: 243.22 kDa
Released: 1 Feb 2017

Explore 5TJ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TJ2 contains 131 α-helices and 102 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: 33 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
α-helix	17-31	15
β-strand	34-38	5	1
α-helix	43-52	10
β-strand	59-63	5	1
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	2
α-helix	77-79	3
α-helix	83-87	5
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	145-147	3	5
α-helix	154-163	10
β-strand	167-172	6	7
β-strand	175-182	8	7
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	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
α-helix	257	1
β-strand	258-259	2	8
β-strand	260-266	7	1
β-strand	267	1	2
α-helix	273-279	7
α-helix	280-284	5
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	8
α-helix	330-331	2
α-helix	335-352	18
α-helix	357-1224	19
α-helix	1249-1261	13
α-helix	1265-1278	14
α-helix	1282-1298	17
α-helix	1304-1307	4
α-helix	1309-1313	5
β-strand	1315	1	9
β-strand	1321	1	9
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1366	12
α-helix	1370-1372	3
α-helix	1384-1404	21

Chain B: 33 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	10
α-helix	17-31	15
β-strand	34-38	5	10
α-helix	43-52	10
β-strand	59-63	5	10
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	11
α-helix	77-79	3
α-helix	83-87	5
β-strand	89	1	12
α-helix	91-96	6
β-strand	98-99	2	13
β-strand	102-103	2	13
β-strand	106-111	6	10
β-strand	114-118	5	14
β-strand	128	1	15
α-helix	132-142	11
β-strand	145-147	3	14
α-helix	154-163	10
β-strand	167-172	6	16
β-strand	175-182	8	16
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	14
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	14
α-helix	246-248	3
β-strand	249-250	2	15
β-strand	253-254	2	15
α-helix	257	1
β-strand	258-259	2	17
β-strand	260-266	7	10
β-strand	267	1	11
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	10
β-strand	304	1	12
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	17
α-helix	330-331	2
α-helix	335-352	18
α-helix	357-1224	19
β-strand	1229	1	18
α-helix	1249-1261	13
α-helix	1265-1278	14
α-helix	1282-1298	17
α-helix	1304-1307	4
α-helix	1309-1313	5
β-strand	1315	1	19
β-strand	1321	1	19
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1366	12
α-helix	1370-1374	5
α-helix	1384-1404	21

Chain C: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	20
α-helix	17-31	15
β-strand	34-38	5	20
α-helix	43-52	10
β-strand	59-63	5	20
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	21
α-helix	77-79	3
α-helix	83-87	5
β-strand	89	1	22
α-helix	91-96	6
β-strand	98-99	2	23
β-strand	102-103	2	23
β-strand	106-111	6	20
β-strand	114-118	5	24
β-strand	128	1	25
α-helix	132-142	11
β-strand	145-147	3	24
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	24
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	24
α-helix	246-248	3
β-strand	249-250	2	25
β-strand	253-254	2	25
α-helix	257	1
β-strand	258-259	2	26
β-strand	260-266	7	20
β-strand	267	1	21
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	20
β-strand	304	1	22
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	26
α-helix	330-331	2
α-helix	335-352	18
α-helix	357-1224	19
β-strand	1229	1	16
α-helix	1249-1261	13
α-helix	1265-1278	14
α-helix	1282-1298	17
α-helix	1304-1307	4
α-helix	1309-1313	5
β-strand	1315	1	27
β-strand	1321	1	27
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1365	11
α-helix	1384-1402	19

Chain D: 33 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	6-10	5	28
α-helix	17-31	15
β-strand	34-38	5	28
α-helix	43-52	10
β-strand	59-63	5	28
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	29
α-helix	77-79	3
α-helix	83-87	5
β-strand	89	1	30
α-helix	91-96	6
β-strand	98-99	2	31
β-strand	102-103	2	31
β-strand	106-111	6	28
β-strand	114-118	5	32
β-strand	128	1	33
α-helix	132-141	10
β-strand	145-147	3	32
α-helix	154-163	10
β-strand	167-172	6	34
β-strand	175-182	8	34
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	32
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	32
α-helix	246-248	3
β-strand	249-250	2	33
β-strand	253-254	2	33
α-helix	257	1
β-strand	258-259	2	35
β-strand	260-266	7	28
β-strand	267	1	29
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	28
β-strand	304	1	30
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	35
α-helix	330-331	2
α-helix	335-352	18
α-helix	357-1224	19
α-helix	1252-1261	10
α-helix	1265-1278	14
α-helix	1282-1298	17
α-helix	1304-1307	4
α-helix	1309-1313	5
β-strand	1315	1	36
β-strand	1321	1	36
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1365	11
α-helix	1384-1404	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein	A, B, C, D	protein	553	Escherichia coli, Homo sapiens	Q8TAX9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5TJ2_1 Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein (chains A, B, C, D)
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAA
LAAAQTNAAAMSAGLDIHFRGKTKSFPEGKSLGSEDSRNMKEKLEDMESVLKDLTEEKRK
DVLNSLAKCLGKEDIRQDLEQRVSEVLISGELHMEDSDKPLLSSLFNAAGVLVEARAKAI
LDFLDALLELSEEQQFVAEALEKGTLPLLKDQVKSVMEQNWDELASSPPDPEARILCALY
VVVSILLELAEGP

Primary citation

Human Gasdermin-B and disease: Sulfatide Binding, Caspase cleavage, and Structural impact of Asthma- and IBS-Associated Polymorphism. Chao, L.K., Kulakova, L., Herzberg, O. Proc Natl Acad Sci U S A (2017). DOI 10.1073/pnas.1616783114

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
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
5TJ4 3.5 Å, Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Pro306 fused…
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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