5TIB: PDB entry 5TIB

Gasdermin-B C-terminal domain containing the polymorphism residues Arg299:Ser306 fused to maltose binding protein. Determined by X-ray diffraction at 2.6 Å resolution. Released 1 Feb 2017.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 2
Atoms: 8,238
Mol. weight: 122.94 kDa
Released: 1 Feb 2017

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

Secondary structure: helices and β-sheets

5TIB contains 64 α-helices and 53 β-strands across 2 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, 26 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	6-10	5	1
α-helix	17-31	15
β-strand	34-38	5	1
α-helix	43-51	9
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	83-86	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	145-147	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
β-strand	1229	1	9
α-helix	1249-1261	13
α-helix	1265-1276	12
α-helix	1282-1298	17
α-helix	1303-1305	3
α-helix	1309-1313	5
β-strand	1315	1	10
β-strand	1321	1	10
α-helix	1323-1337	15
α-helix	1342-1352	11
α-helix	1355-1365	11
α-helix	1384-1404	21

Chain B: 31 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	11
α-helix	17-31	15
β-strand	34-38	5	11
α-helix	43-52	10
β-strand	59-63	5	11
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	12
α-helix	83-86	4
β-strand	89	1	13
α-helix	91-96	6
β-strand	98-99	2	14
β-strand	102-103	2	14
β-strand	106-111	6	11
β-strand	114-118	5	15
β-strand	128	1	16
α-helix	132-141	10
β-strand	145-147	3	15
α-helix	154-163	10
β-strand	167-172	6	9
β-strand	175-182	8	9
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	15
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	15
α-helix	246-248	3
β-strand	249	1	16
β-strand	250	1	17
β-strand	253	1	17
α-helix	257	1
β-strand	258-259	2	18
β-strand	260-266	7	11
β-strand	267	1	12
α-helix	273-277	5
α-helix	278-284	7
α-helix	287-296	10
β-strand	301-302	2	11
β-strand	304	1	13
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	18
α-helix	330-331	2
α-helix	336-352	17
α-helix	357-1223	18
β-strand	1229	1	7
α-helix	1249-1261	13
α-helix	1265-1277	13
α-helix	1282-1298	17
α-helix	1303-1305	3
α-helix	1309-1312	4
β-strand	1315	1	19
β-strand	1321	1	19
α-helix	1323-1338	16
α-helix	1342-1352	11
α-helix	1355-1364	10
α-helix	1384-1403	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sugar ABC transporter substrate-binding protein,Gasdermin-B	A, B	protein	557	Escherichia coli, Homo sapiens	Q8TAX9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5TIB_1 Sugar ABC transporter substrate-binding protein,Gasdermin-B (chains A, B)
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAA
LAAAQTNAAAMSAGLDIHFRGKTKSFPEGKSLGSEDSRNMKEKLEDMESVLKDLTEEKRK
DVLNSLAKCLGKEDIRQDLEQRVSEVLISRELHMEDSDKPLLSSLFNAAGVLVEARAKAI
LDFLDALLELSEEQQFVAEALEKGTLPLLKDQVKSVMEQNWDELASSPPDMDYDPEARIL
CALYVVVSILLELAEGP

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:

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
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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