PDB-6ao3: Crystal structure of the murine gasdermin D C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 6ao3

Title

Crystal structure of the murine gasdermin D C-terminal domain

Components

Gasdermin-D

Keywords

IMMUNE SYSTEM / Inflammasome / pyroptosis / gasdermin D / autoinhibition / Salmonella infection

Function / homology

Function and homology information

Release of apoptotic factors from the mitochondria / Pyroptosis / Regulation of TLR by endogenous ligand / Interleukin-1 processing / pore complex assembly / : / wide pore channel activity / NLRP3 inflammasome complex / cardiolipin binding / phosphatidic acid binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.76 Å

Authors

Liu, Z. / Wang, C. / Yang, J. / Xiao, T.S.

Funding support

United States, 1items

Citation

Journal: Structure / Year: 2018
Title: Structures of the Gasdermin D C-Terminal Domains Reveal Mechanisms of Autoinhibition.
Authors: Liu, Z. / Wang, C. / Rathkey, J.K. / Yang, J. / Dubyak, G.R. / Abbott, D.W. / Xiao, T.S.

History

Deposition	Aug 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 11, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ao3.cif.gz	319.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6ao3.ent.gz	262.7 KB	Display	PDB format
PDBx/mmJSON format	6ao3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ao3_validation.pdf.gz	444.1 KB	Display	wwPDB validaton report
Full document	6ao3_full_validation.pdf.gz	448.3 KB	Display
Data in XML	6ao3_validation.xml.gz	34.4 KB	Display
Data in CIF	6ao3_validation.cif.gz	50.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ao/6ao3 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/6ao3	HTTPS FTP

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Related structure data

Related structure data	6ao4C C: citing same article (ref.)
Similar structure data	5dc4-d 3sl9-4 1oyu-1 3fao-d 6zpk-d 3r26-d 3ro3-d 2c6r-d 2h5y-3 3lk0-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6ao4C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (2) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #88 - Apr 2007 Clathrin similarity (1) #166 - Oct 2013 Proteasome similarity (1) #176 - Aug 2014 Dynein similarity (1) #177 - Sep 2014 Apoptosomes similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1)

Deposited unit

A: Gasdermin-D

B: Gasdermin-D

C: Gasdermin-D

D: Gasdermin-D

92.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gasdermin-D

defined by author&software
Evidence: gel filtration
23 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Gasdermin-D

defined by author&software
23 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Gasdermin-D

defined by author&software
23 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Gasdermin-D

defined by author&software
23 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.300, 56.840, 81.840
Angle α, β, γ (deg.)	94.86, 102.79, 98.99
Int Tables number	1
Space group name H-M	P1

#1: Protein	Gasdermin-D / Gasdermin domain-containing protein 1 Mass: 23013.174 Da / Num. of mol.: 4 / Fragment: unp residues 277-487 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus RIPL / References: UniProt: Q9D8T2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Gasdermin-D / Gasdermin domain-containing protein 1

Mass: 23013.174 Da / Num. of mol.: 4 / Fragment: unp residues 277-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus RIPL / References: UniProt: Q9D8T2

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.78 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% (v/v) polyethylene glycol (PEG) 3350, 0.1 M Bis-Tris (pH 5.5), 0.2 M MgCl2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.76→79.2 Å / Num. obs: 75173 / % possible obs: 97.1 % / Redundancy: 2.93 % / CC_1/2: 0.995 / Net I/σ(I): 10.1
Reflection shell	Resolution: 1.76→1.81 Å / Redundancy: 2.88 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 5506 / CC_1/2: 0.555 / % possible all: 95.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.76→34.76 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.93

	R_factor	Num. reflection	% reflection
R_free	0.1857	3575	4.99 %
R_work	0.1613	-	-
obs	0.1625	71700	92.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.76→34.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6021	0	0	587	6608

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6125
X-RAY DIFFRACTION	f_angle_d	1.016	8353
X-RAY DIFFRACTION	f_dihedral_angle_d	17.007	3733
X-RAY DIFFRACTION	f_chiral_restr	0.059	1009
X-RAY DIFFRACTION	f_plane_restr	0.007	1071

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.76-1.7832	0.2573	125	0.2494	2264	X-RAY DIFFRACTION	81
1.7832-1.8076	0.2616	123	0.2391	2384	X-RAY DIFFRACTION	83
1.8076-1.8334	0.2359	132	0.2171	2331	X-RAY DIFFRACTION	83
1.8334-1.8608	0.2512	137	0.2077	2368	X-RAY DIFFRACTION	85
1.8608-1.8898	0.216	133	0.1993	2463	X-RAY DIFFRACTION	86
1.8898-1.9208	0.2405	119	0.1951	2419	X-RAY DIFFRACTION	87
1.9208-1.9539	0.2182	149	0.1872	2525	X-RAY DIFFRACTION	88
1.9539-1.9895	0.2341	125	0.1811	2558	X-RAY DIFFRACTION	91
1.9895-2.0277	0.2062	126	0.1715	2602	X-RAY DIFFRACTION	92
2.0277-2.0691	0.2051	127	0.1675	2593	X-RAY DIFFRACTION	92
2.0691-2.1141	0.2152	130	0.1671	2663	X-RAY DIFFRACTION	93
2.1141-2.1633	0.2047	135	0.1645	2686	X-RAY DIFFRACTION	94
2.1633-2.2174	0.1786	141	0.1548	2628	X-RAY DIFFRACTION	94
2.2174-2.2773	0.1751	150	0.1482	2711	X-RAY DIFFRACTION	95
2.2773-2.3443	0.1807	145	0.1527	2641	X-RAY DIFFRACTION	95
2.3443-2.42	0.1961	144	0.1666	2698	X-RAY DIFFRACTION	96
2.42-2.5064	0.2149	133	0.1656	2739	X-RAY DIFFRACTION	96
2.5064-2.6067	0.1962	133	0.1587	2754	X-RAY DIFFRACTION	97
2.6067-2.7253	0.1736	133	0.1581	2777	X-RAY DIFFRACTION	97
2.7253-2.869	0.1777	139	0.1597	2753	X-RAY DIFFRACTION	98
2.869-3.0486	0.1746	156	0.1538	2784	X-RAY DIFFRACTION	98
3.0486-3.2838	0.1834	145	0.1553	2762	X-RAY DIFFRACTION	98
3.2838-3.614	0.1785	154	0.1447	2734	X-RAY DIFFRACTION	98
3.614-4.1362	0.1555	148	0.1351	2793	X-RAY DIFFRACTION	98
4.1362-5.2084	0.1514	147	0.1424	2749	X-RAY DIFFRACTION	98
5.2084-34.7672	0.1839	146	0.1801	2746	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.2218	-1.5182	2.2431	4.0505	-1.819	6.7359	0.1454	0.1568	-0.0408	-0.24	-0.0422	0.0505	-0.0325	0.0752	-0.0986	0.1818	-0.0038	0.0372	0.1129	-0.0226	0.1299	27.1408	30.4166	69.9067
2	3.7867	0.2878	-0.5756	5.6265	0.6878	1.6016	-0.0026	0.1124	0.1861	-0.2407	-0.0022	0.1157	-0.0393	-0.0713	0.022	0.1653	0.0365	-0.0191	0.1291	0.0387	0.1713	13.4592	45.251	68.9126
3	3.418	0.5365	2.0818	3.1205	1.182	3.4062	-0.1633	0.0149	0.3599	-0.0905	0.068	-0.0866	-0.196	0.096	0.0873	0.1429	0.0304	-0.0051	0.1293	-0.0047	0.1786	23.7312	43.0884	76.0536
4	2.2606	-0.3969	0.7631	1.3903	-0.2532	1.4415	-0.0456	-0.1414	0.235	0.0739	0.0303	-0.1972	-0.0814	0.1361	-0.0026	0.1563	0.022	-0.0142	0.1618	-0.0508	0.1953	37.6835	38.2229	83.2057
5	3.3235	-0.5414	-2.7795	3.3308	1.6371	7.2149	0.1286	0.0615	0.1299	-0.143	-0.0244	-0.0533	-0.1973	-0.0233	-0.1821	0.158	0.0148	-0.0278	0.1123	0.0301	0.1328	15.8708	27.3267	69.4957
6	3.3692	-1.6181	1.2583	7.4044	-4.4918	8.3905	0.1284	0.2619	-0.3382	-0.3202	-0.0023	0.4909	0.16	-0.0618	-0.2249	0.1363	0.0028	-0.0091	0.1269	-0.0303	0.183	20.8416	9.9967	62.7616
7	5.0336	3.3159	-0.4091	2.9733	-1.5869	2.4696	0.1833	-0.2637	0.0282	0.5265	-0.091	0.0137	-0.1344	0.0416	-0.0882	0.1857	0.0448	0.0128	0.1689	-0.0066	0.1506	32.5171	14.61	72.0197
8	4.3564	2.3341	0.3686	7.2462	-0.2754	2.2149	-0.1636	0.2742	-0.2673	-0.2838	0.2202	-0.3609	0.1577	0.3523	-0.0651	0.1844	0.0186	0.0534	0.2057	-0.0412	0.1607	33.6928	11.6362	62.7596
9	4.2146	0.4887	-2.0392	2.1028	0.1869	3.2278	-0.0722	0.1627	0.0271	-0.2557	0.0976	-0.1449	-0.0282	0.1072	-0.0536	0.1145	-0.0071	0.0131	0.1216	0.0103	0.0998	28.5964	19.8806	66.3699
10	5.5478	0.6169	0.7582	4.0192	0.9822	6.2245	0.0188	0.3048	-0.4689	-0.1795	-0.1244	0.1178	0.3418	0.1281	0.069	0.1568	0.0478	0.023	0.1379	0.0003	0.1919	14.119	7.378	73.608
11	2.0877	-1.1526	-1.701	4.7296	4.2621	7.7931	0.1069	0.1583	-0.31	-0.053	-0.1009	0.3185	-0.1449	-0.4618	-0.0155	0.0927	0.0176	-0.0025	0.1539	0.0232	0.157	4.5464	18.779	74.7953
12	1.3544	0.2937	-0.2909	1.7173	0.3083	2.3489	0.1672	-0.2019	0.0032	0.0891	-0.1501	0.082	0.1007	-0.2073	-0.0629	0.1428	0.0332	-0.0237	0.1651	0.0249	0.1294	1.425	21.4082	83.9279
13	2.934	0.4545	-0.3007	3.4179	0.806	1.4326	0.0691	-0.089	-0.2906	0.1142	-0.0849	0.0571	0.1726	-0.0476	0.0173	0.1381	0.0027	-0.007	0.1563	0.0522	0.1149	2.7074	10.7303	84.3941
14	2.5859	-0.9251	-2.7188	1.8624	1.1202	7.0941	0.0269	-0.0745	0.0314	0.0516	0.0539	0.1015	-0.0773	0.0224	-0.0726	0.1082	0.0019	0.0075	0.092	0.0092	0.1377	13.8392	19.451	76.1196
15	2.4696	1.0897	1.0495	4.0001	0.9194	1.9476	0.0479	-0.1413	0.1505	0.2046	-0.1072	0.1689	0.0541	-0.0388	0.0553	0.112	-0.0003	0.0411	0.1856	0.0012	0.1787	41.049	22.8555	43.0278
16	5.6559	-3.5807	1.8038	3.29	-2.9768	4.0741	0.2008	0.5253	0.1868	-0.4855	-0.2632	-0.192	0.0471	0.1293	0.0609	0.179	-0.0182	-0.0179	0.257	0.0111	0.1735	55.3586	26.8884	36.6691
17	5.7047	-1.9728	0.03	6.0359	-0.6991	3.0245	-0.0638	-0.5785	0.6564	0.4061	0.0698	-0.3836	-0.4326	0.37	-0.0047	0.1738	-0.0347	-0.0295	0.2209	-0.0382	0.21	56.1802	30.4894	45.7769
18	3.3842	-0.4421	1.4691	1.3195	-0.1715	1.9267	-0.0046	-0.0903	0.1587	0.1098	-0.0017	0.0501	-0.0576	0.0913	0.039	0.1204	-0.0219	0.0103	0.1404	-0.0039	0.1161	45.1922	27.1194	39.1814
19	2.0103	-0.7205	0.1311	2.7811	1.42	2.4228	0.1644	0.1817	-0.0832	-0.0635	-0.0069	-0.0689	0.1677	-0.1997	-0.095	0.1664	-0.0291	-0.0014	0.2181	0.0293	0.1639	26.1584	20.1634	29.503
20	3.4236	0.0752	0.3671	3.6843	0.6518	3.7546	-0.0461	0.1813	0.2019	-0.069	-0.0096	0.1128	-0.119	-0.0315	0.011	0.1533	-0.0078	-0.0093	0.2229	0.0716	0.1073	25.3664	29.7086	24.4932
21	3.5151	1.0212	2.8615	3.5162	1.0753	6.7634	0.0028	0.006	-0.0535	0.0062	-0.0316	-0.053	-0.074	0.1152	0.023	0.086	0.0095	0.008	0.1266	0.0115	0.1759	36.586	21.9622	34.0359
22	2.9017	1.0717	-0.7789	4.0611	-0.0393	1.4131	0.0515	-0.2872	-0.7139	0.5944	-0.2049	-0.1723	0.1072	0.147	0.0177	0.2553	0.0217	-0.0141	0.1961	0.0235	0.3486	47.9184	3.2634	42.1915
23	2.7385	0.0937	1.0912	4.6171	0.243	1.8508	-0.1662	0.2146	-0.7208	0.5363	0.0196	0.4271	0.1796	-0.1513	0.0651	0.274	-0.0576	0.1159	0.2418	0.006	0.5091	32.9303	-2.9648	39.9062
24	2.8308	-0.4295	-0.3039	3.8392	0.9067	3.1997	-0.1603	0.1216	-0.8702	0.3653	0.053	0.0156	0.2789	-0.069	0.1253	0.1835	-0.0327	0.028	0.1424	-0.0412	0.3789	42.9617	-0.8429	38.3854
25	3.2308	-0.8196	0.4645	1.5851	-0.9616	2.6616	0.0378	0.2853	-0.5119	-0.0926	0.1133	-0.305	-0.103	0.439	-0.2633	0.2284	-0.0719	0.0359	0.2864	-0.1593	0.391	63.0016	5.8413	29.4345
26	2.8138	0.1272	-0.4116	2.8404	0.6212	1.4102	0.0911	0.4918	-0.7535	0.0688	-0.2525	-0.2723	0.0833	-0.0126	-0.124	0.3286	-0.0628	0.0243	0.4265	-0.2536	0.5428	63.4586	-2.5539	22.8614
27	3.0488	0.1148	-1.0189	2.6442	-0.1058	2.9999	-0.0985	0.4181	-0.5807	0.0504	0.084	-0.3087	-0.101	-0.0415	-0.0028	0.1872	-0.0373	0.0183	0.2175	-0.0749	0.27	52.2518	4.7248	32.5275

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 286 through 307 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 308 through 367 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 368 through 399 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 400 through 484 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 286 through 307 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 308 through 324 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 325 through 341 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 342 through 358 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 359 through 383 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 384 through 399 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 400 through 414 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 415 through 431 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 432 through 462 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 463 through 483 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 287 through 324 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 325 through 341 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 342 through 359 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 360 through 399 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 400 through 430 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 431 through 462 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 463 through 484 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 286 through 324 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 325 through 358 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 359 through 398 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 399 through 431 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 432 through 462 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 463 through 483 )

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi