PDB-7n52: Structure of a bacterial gasdermin from Runella zeae

ID or keywords:

Entry

Database: PDB / ID: 7n52

Title

Structure of a bacterial gasdermin from Runella zeae

Components

Gasdermin

Keywords

IMMUNE SYSTEM / gasdermin / immunity / membrane / pore-forming protein / lipid binding protein / palmitoylation

Biological species

Runella zeae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.9 Å

Authors

Johnson, A.G. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Science / Year: 2022
Title: Bacterial gasdermins reveal an ancient mechanism of cell death.
Authors: Johnson, A.G. / Wein, T. / Mayer, M.L. / Duncan-Lowey, B. / Yirmiya, E. / Oppenheimer-Shaanan, Y. / Amitai, G. / Sorek, R. / Kranzusch, P.J.

History

Deposition	Jun 4, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 23, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 26, 2022	Group: Database references / Category: citation / citation_author / 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	7n52.cif.gz	487.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7n52.ent.gz		Display	PDB format
PDBx/mmJSON format	7n52.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7n52_validation.pdf.gz	459.1 KB	Display	wwPDB validaton report
Full document	7n52_full_validation.pdf.gz	475.5 KB	Display
Data in XML	7n52_validation.xml.gz	36.8 KB	Display
Data in CIF	7n52_validation.cif.gz	47.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n5/7n52 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/7n52	HTTPS FTP

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Related structure data

Related structure data	7n50C 7n51C C: citing same article (ref.)
Similar structure data	4cnm-d 1hk7-1 1pw6-4 6tbo-d 5m7q-d 4zua-1 2c9c-d 6t71-d 6abm-d 2fnp-d 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)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Gasdermin

B: Gasdermin

C: Gasdermin

D: Gasdermin

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

1

A: Gasdermin

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

2

B: Gasdermin

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

3

C: Gasdermin

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

4

D: Gasdermin

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

Unit cell

Length a, b, c (Å)	69.290, 103.852, 78.992
Angle α, β, γ (deg.)	90.000, 111.544, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Gasdermin Mass: 30702.480 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Runella zeae (bacteria) / Production host: Escherichia coli (E. coli)
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.86 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 150 mM DL-malic acid (pH 7.6), 16% PEG-3350, and 10% Silver Bullets A1 solution (1,5-Naphthalenedisulfonic acid disodium salt, 2,5-Pyridinedicarboxylic acid, 3,5-Dinitrosalicylic acid, HEPES- ...Details: 150 mM DL-malic acid (pH 7.6), 16% PEG-3350, and 10% Silver Bullets A1 solution (1,5-Naphthalenedisulfonic acid disodium salt, 2,5-Pyridinedicarboxylic acid, 3,5-Dinitrosalicylic acid, HEPES-NaOH pH 6.8) (Hampton)

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.86 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 150 mM DL-malic acid (pH 7.6), 16% PEG-3350, and 10% Silver Bullets A1 solution (1,5-Naphthalenedisulfonic acid disodium salt, 2,5-Pyridinedicarboxylic acid, 3,5-Dinitrosalicylic acid, HEPES- ...

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 2.9→42.4 Å / Num. obs: 23133 / % possible obs: 99.5 % / Redundancy: 26.5 % / B_iso Wilson estimate: 56.37 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.06 / Net I/σ(I): 12.7
Reflection shell	Resolution: 2.9→3.07 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3645 / CC_1/2: 0.941 / R_pim(I) all: 0.431

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Processing

Software

Name	Version	Classification
PHENIX	1.19.1_4122	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.9→42.4 Å / SU ML: 0.4082 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2795	2003	8.69 %
R_work	0.237	21041	-
obs	0.2407	23004	99.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 65.96 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→42.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7994	0	0	0	7994

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	8119
X-RAY DIFFRACTION	f_angle_d	0.5809	10888
X-RAY DIFFRACTION	f_chiral_restr	0.0454	1230
X-RAY DIFFRACTION	f_plane_restr	0.0041	1370
X-RAY DIFFRACTION	f_dihedral_angle_d	14.4653	3051

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 (%)
2.9-2.97	0.3806	137	0.319	1417	X-RAY DIFFRACTION	95.45
2.97-3.05	0.3948	135	0.3074	1509	X-RAY DIFFRACTION	98.86
3.05-3.14	0.3546	146	0.3041	1483	X-RAY DIFFRACTION	98.85
3.14-3.24	0.351	149	0.3022	1471	X-RAY DIFFRACTION	99.39
3.24-3.36	0.3198	126	0.2782	1531	X-RAY DIFFRACTION	99.22
3.36-3.49	0.3223	152	0.2651	1496	X-RAY DIFFRACTION	99.34
3.49-3.65	0.3441	152	0.249	1501	X-RAY DIFFRACTION	99.34
3.65-3.84	0.2594	144	0.2493	1501	X-RAY DIFFRACTION	99.4
3.84-4.08	0.2171	128	0.224	1507	X-RAY DIFFRACTION	99.57
4.08-4.4	0.2578	147	0.2029	1518	X-RAY DIFFRACTION	99.7
4.4-4.84	0.2583	147	0.1792	1500	X-RAY DIFFRACTION	99.76
4.84-5.54	0.2112	144	0.2177	1527	X-RAY DIFFRACTION	99.7
5.54-6.97	0.3057	147	0.2393	1533	X-RAY DIFFRACTION	99.7
6.97-42.4	0.2486	149	0.2228	1547	X-RAY DIFFRACTION	99.76

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	3.15842188353	-2.41150202939	2.00226554452	3.751762238	-0.447343476783	1.88645674845	0.199117586275	0.724226887117	0.678173481412	-0.273288987064	-0.280413720243	0.129619622972	0.0390419371167	0.301441010251	0.143748363448	0.523005893421	0.0550315161761	0.0787740616014	0.434094299507	0.0085821159239	0.463689326474	-11.665968499	50.5776353975	17.06471787
2	2.73984635524	-0.979619636124	0.494340073337	1.68312561798	0.258778080189	0.787707327985	0.041769990362	-0.365170855626	0.0454359640627	-0.0607862221858	0.0843898262712	-0.0921921459139	-0.0500976368838	0.39746597049	0.0193006092139	0.286578225694	-0.050172689151	-0.00504664702581	0.41568487964	-0.0370951483415	0.462252953726	-3.30971176219	48.3071565723	20.5743455852
3	3.75153429149	1.29103083289	-0.465417030951	2.82981729181	-0.982091576116	3.8888650675	0.358782481814	0.197014256311	0.535682914497	-0.202735484986	-0.14887314364	-0.00633586502027	-0.2762999466	-0.430733824995	-0.132672380947	0.335411297628	0.114306843866	0.0149478203764	0.501052273727	0.010230476625	0.390794314161	-6.48824813123	30.7437383582	39.4399963766
4	3.89185527162	0.308067862883	-0.423114995959	3.78940250532	1.96723937618	3.10383086105	-0.259334303334	0.07992701597	0.00582895544073	0.189397409721	0.324101577941	-0.425332590231	0.00949809443611	0.284155210363	0.00503362648387	0.370983872986	-0.0242827551714	0.070198454681	0.503617767782	0.129923813534	0.401522307804	-0.488871652922	26.8988747078	37.6680247966
5	0.753151258488	0.22231918131	1.11364492104	0.948369450041	0.853800089764	0.791560923396	0.232901063188	-0.586038600186	-0.991598009859	0.0405987329096	-0.367260222984	0.499519135838	0.0855039890025	-0.218643129481	0.21138187975	0.577104449615	0.0944506585981	0.097125116856	1.01585860598	0.143994061341	0.944889393847	-17.3428575772	28.3776530503	40.5618077255
6	1.94980584227	-0.890755431243	-0.101859559067	1.043262954	-0.449033182683	2.87685131213	0.0270048489745	-0.0657033983206	0.0106146551225	-0.0579775469619	0.0243561175944	0.0501810070905	-0.140115403595	-0.069346146904	-0.154511177333	0.294761457784	0.106237111226	0.121779277884	0.43644667485	-0.0301354394952	0.399456002711	-6.24744241705	30.1875509847	37.2547871155
7	2.894768047	1.20892833112	0.0700884989561	0.90818974708	1.80424237555	3.58623004502	0.541334986591	-0.876068466591	1.27436854684	0.0356541713128	-1.37810503627	0.483192975177	-0.200421979678	-1.39047347567	0.14187049655	0.393054282502	0.00153668315286	0.0148777632122	0.318738087624	-0.181375104165	0.817865076726	-6.29871469246	24.4449954628	-6.01267720669
8	7.75900809961	0.855265365197	2.11744737269	1.9364902926	0.858841100845	1.91557365506	1.15159146235	-3.23371675259	3.70088289005	1.15025467034	-0.401752989086	-0.761047469389	-1.40318579211	-0.33945298192	0.335806653569	0.537589043529	-0.0675827310479	0.144542875343	0.230656582369	-0.372485087766	0.9957973989	5.69880266129	32.117904165	2.6835230738
9	3.44521197914	-1.19929247192	1.37238320568	2.63208998321	1.36388414933	0.432021905162	0.0244351736594	0.246065013132	0.292280446061	0.142691752136	-0.0342449343252	0.199172885856	0.0699527560996	-0.296522620676	0.0407631536654	0.409851438968	-0.0182500841788	-0.0304688629012	0.484253284725	-0.054894648688	0.528697182718	-9.32708890108	28.1057865881	-3.04204896836
10	5.07752338681	0.143066471835	-3.07193164783	2.74730556745	0.644162266461	1.65833249155	-0.201133303191	0.119557803256	0.952555443369	-0.0992649900407	0.29765831042	-0.139546139983	-0.334035007822	0.185390138872	-0.128334602886	0.481112257433	0.0380618242347	0.0382771301716	0.263921116387	-0.00666761347314	0.506484549041	5.68825991139	28.6384279987	-7.31386343149
11	1.70608057632	0.182434244626	-0.974478608078	2.32640448166	-1.29681307775	1.48896227869	-0.617467288103	0.0225522460549	0.0614691159105	-0.443509187425	0.286304303461	0.344825217709	0.776433877455	-0.178968638582	-1.04101759843	0.372871335677	-0.00826717370618	-0.0255108998086	1.11482712634	-0.194309864767	1.03075806661	-29.4522972353	26.2782768169	-6.38641888194
12	3.20886698683	-0.174049589642	-1.39582157105	0.63385969232	0.0352078488384	2.19192240033	0.0847093122198	0.154137290765	0.093563396009	-0.127319445582	-0.0430897637958	-0.13456228587	0.130425228682	-0.224523686234	2.31761853973	0.442731285069	-0.0745612071487	-0.0255811384983	0.231993037613	-0.149116808807	0.552210757271	-3.32392625391	23.7916496682	-5.42944172994
13	4.53406017863	-1.83115072462	1.22377385036	2.67653592261	0.543255051664	0.893830257943	-0.345486559835	-0.246902932385	0.178356373067	0.00760362596954	0.0369617849755	0.431025788882	-0.27406509774	-0.0250795551241	0.209585774074	0.492958182929	-0.18363000689	0.0497370578623	0.450607998276	0.0361112372671	0.644885729001	-5.64453591958	5.69273125393	12.9693208384
14	2.28390816748	0.903389143681	-0.00944524955364	1.39880486484	1.48226148461	1.67857636352	0.530914645995	-1.21908288568	0.186196850302	0.807987216485	-0.613563277099	-0.115355678099	0.15681771605	0.355450836544	-0.138972111419	0.554159713414	-0.0731950791958	0.00351896972829	0.725470312249	-0.0345610882127	0.664003313739	-18.9862316331	13.9796389709	22.9231555134
15	2.78319396269	1.13719578645	-0.168667499601	1.33453944802	-1.3868858021	1.51183791269	-0.0464563197494	-0.355593803158	-0.606395560264	0.0943346045999	-0.0221733683292	-0.0119292978017	0.489136963278	-0.0970910131194	-0.103087707277	0.528237225445	0.0116000175417	-0.0217207687594	0.38251512254	-0.0217194478226	0.959593496203	-3.45083551705	3.26531075032	14.5932020608
16	3.71750643191	1.19168290189	-0.645956586942	3.15910366293	1.33680449715	2.06548014893	0.138142880176	-1.35592575099	0.0015377709979	0.42612692458	-0.469875715673	0.669829555309	0.37751285738	-0.0818695994067	0.308919476408	0.47316601983	-0.036139243592	0.0898736059805	0.638881343112	0.0949172427014	1.13836700748	-13.2005986634	5.8656056382	16.4007091413
17	2.6957214744	0.948042760513	-0.287328230871	1.9481842505	0.72891155214	1.30076271104	0.139293261789	-0.402105406274	0.00129195133635	0.138577576289	-0.251982801488	0.0415984308587	0.0509582265472	-0.10096037098	0.0204638374779	0.450491919886	-0.0447761375534	0.0258800916114	0.446179373555	-0.038791391839	0.610423669544	-3.58191356195	7.17740827414	13.3810592053
18	4.50038167857	-0.637625265824	0.813248044674	2.63540128557	-0.0473221730909	2.16201292934	0.0619220702371	0.275202282488	-0.500731014603	-0.241418027239	0.14945576282	-0.00141114121161	0.174902349852	0.325310640362	-0.0514509244662	0.401312007944	0.0714381373966	0.0505377351093	0.20552466635	0.0362093306387	0.425406447889	-8.54829099136	47.4071009791	16.8612736372

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid 110 through 174 )	C	C	110 - 174	110 - 174
2	2	chain 'C' and (resid 175 through 268 )	C	C	175 - 268	175 - 255
3	3	chain 'D' and (resid 2 through 30 )	D	D	2 - 30	1 - 29
4	4	chain 'D' and (resid 31 through 156 )	D	D	31 - 156	30 - 147
5	5	chain 'D' and (resid 157 through 182 )	D	D	157 - 182	148 - 171
6	6	chain 'D' and (resid 183 through 268 )	D	D	183 - 268	172 - 246
7	7	chain 'A' and (resid 2 through 30 )	A	A	2 - 30	1 - 29
8	8	chain 'A' and (resid 31 through 56 )	A	A	31 - 56	30 - 51
9	9	chain 'A' and (resid 57 through 112 )	A	A	57 - 112	52 - 100
10	10	chain 'A' and (resid 113 through 166 )	A	A	113 - 166	101 - 154
11	11	chain 'A' and (resid 167 through 184 )	A	A	167 - 184	155 - 172
12	12	chain 'A' and (resid 185 through 268 )	A	A	185 - 268	173 - 250
13	13	chain 'B' and (resid 1 through 30 )	B	B	1 - 30	1 - 30
14	14	chain 'B' and (resid 31 through 55 )	B	B	31 - 55	31 - 55
15	15	chain 'B' and (resid 56 through 99 )	B	B	56 - 99	56 - 92
16	16	chain 'B' and (resid 100 through 154 )	B	B	100 - 154	93 - 142
17	17	chain 'B' and (resid 155 through 268 )	B	B	155 - 268	143 - 236
18	18	chain 'C' and (resid 1 through 109 )	C	C	1 - 109	1 - 109

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