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

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Basic information

Entry
Database: PDB / ID: 7n52
TitleStructure of a bacterial gasdermin from Runella zeae
ComponentsGasdermin
KeywordsIMMUNE SYSTEM / gasdermin / immunity / membrane / pore-forming protein / lipid binding protein / palmitoylation
Biological speciesRunella zeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsJohnson, A.G. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)T32CA207021 United States
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.
#1: Journal: Biorxiv / Year: 2021
Title: Bacterial gasdermins reveal and 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
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gasdermin
B: Gasdermin
C: Gasdermin
D: Gasdermin


Theoretical massNumber of molelcules
Total (without water)122,8104
Polymers122,8104
Non-polymers00
Water00
1
A: Gasdermin


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gasdermin


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gasdermin


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gasdermin


Theoretical massNumber of molelcules
Total (without water)30,7021
Polymers30,7021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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 interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 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)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.9→42.4 Å / Num. obs: 23133 / % possible obs: 99.5 % / Redundancy: 26.5 % / Biso Wilson estimate: 56.37 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 2.9→3.07 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3645 / CC1/2: 0.941 / Rpim(I) all: 0.431

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2795 2003 8.69 %
Rwork0.237 21041 -
obs0.2407 23004 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.96 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7994 0 0 0 7994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00288119
X-RAY DIFFRACTIONf_angle_d0.580910888
X-RAY DIFFRACTIONf_chiral_restr0.04541230
X-RAY DIFFRACTIONf_plane_restr0.00411370
X-RAY DIFFRACTIONf_dihedral_angle_d14.46533051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.38061370.3191417X-RAY DIFFRACTION95.45
2.97-3.050.39481350.30741509X-RAY DIFFRACTION98.86
3.05-3.140.35461460.30411483X-RAY DIFFRACTION98.85
3.14-3.240.3511490.30221471X-RAY DIFFRACTION99.39
3.24-3.360.31981260.27821531X-RAY DIFFRACTION99.22
3.36-3.490.32231520.26511496X-RAY DIFFRACTION99.34
3.49-3.650.34411520.2491501X-RAY DIFFRACTION99.34
3.65-3.840.25941440.24931501X-RAY DIFFRACTION99.4
3.84-4.080.21711280.2241507X-RAY DIFFRACTION99.57
4.08-4.40.25781470.20291518X-RAY DIFFRACTION99.7
4.4-4.840.25831470.17921500X-RAY DIFFRACTION99.76
4.84-5.540.21121440.21771527X-RAY DIFFRACTION99.7
5.54-6.970.30571470.23931533X-RAY DIFFRACTION99.7
6.97-42.40.24861490.22281547X-RAY DIFFRACTION99.76
Refinement TLS params.

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

IDL11 (°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)
13.15842188353-2.411502029392.002265544523.751762238-0.4473434767831.886456748450.1991175862750.7242268871170.678173481412-0.273288987064-0.2804137202430.1296196229720.03904193711670.3014410102510.1437483634480.5230058934210.05503151617610.07877406160140.4340942995070.00858211592390.463689326474-11.66596849950.577635397517.06471787
22.73984635524-0.9796196361240.4943400733371.683125617980.2587780801890.7877073279850.041769990362-0.3651708556260.0454359640627-0.06078622218580.0843898262712-0.0921921459139-0.05009763688380.397465970490.01930060921390.286578225694-0.050172689151-0.005046647025810.41568487964-0.03709514834150.462252953726-3.3097117621948.307156572320.5743455852
33.751534291491.29103083289-0.4654170309512.82981729181-0.9820915761163.88886506750.3587824818140.1970142563110.535682914497-0.202735484986-0.14887314364-0.00633586502027-0.2762999466-0.430733824995-0.1326723809470.3354112976280.1143068438660.01494782037640.5010522737270.0102304766250.390794314161-6.4882481312330.743738358239.4399963766
43.891855271620.308067862883-0.4231149959593.789402505321.967239376183.10383086105-0.2593343033340.079927015970.005828955440730.1893974097210.324101577941-0.4253325902310.009498094436110.2841552103630.005033626483870.370983872986-0.02428275517140.0701984546810.5036177677820.1299238135340.401522307804-0.48887165292226.898874707837.6680247966
50.7531512584880.222319181311.113644921040.9483694500410.8538000897640.7915609233960.232901063188-0.586038600186-0.9915980098590.0405987329096-0.3672602229840.4995191358380.0855039890025-0.2186431294810.211381879750.5771044496150.09445065859810.0971251168561.015858605980.1439940613410.944889393847-17.342857577228.377653050340.5618077255
61.94980584227-0.890755431243-0.1018595590671.043262954-0.4490331826832.876851312130.0270048489745-0.06570339832060.0106146551225-0.05797754696190.02435611759440.0501810070905-0.140115403595-0.069346146904-0.1545111773330.2947614577840.1062371112260.1217792778840.43644667485-0.03013543949520.399456002711-6.2474424170530.187550984737.2547871155
72.8947680471.208928331120.07008849895610.908189747081.804242375553.586230045020.541334986591-0.8760684665911.274368546840.0356541713128-1.378105036270.483192975177-0.200421979678-1.390473475670.141870496550.3930542825020.001536683152860.01487776321220.318738087624-0.1813751041650.817865076726-6.2987146924624.4449954628-6.01267720669
87.759008099610.8552653651972.117447372691.93649029260.8588411008451.915573655061.15159146235-3.233716752593.700882890051.15025467034-0.401752989086-0.761047469389-1.40318579211-0.339452981920.3358066535690.537589043529-0.06758273104790.1445428753430.230656582369-0.3724850877660.99579739895.6988026612932.1179041652.6835230738
93.44521197914-1.199292471921.372383205682.632089983211.363884149330.4320219051620.02443517365940.2460650131320.2922804460610.142691752136-0.03424493432520.1991728858560.0699527560996-0.2965226206760.04076315366540.409851438968-0.0182500841788-0.03046886290120.484253284725-0.0548946486880.528697182718-9.3270889010828.1057865881-3.04204896836
105.077523386810.143066471835-3.071931647832.747305567450.6441622664611.65833249155-0.2011333031910.1195578032560.952555443369-0.09926499004070.29765831042-0.139546139983-0.3340350078220.185390138872-0.1283346028860.4811122574330.03806182423470.03827713017160.263921116387-0.006667613473140.5064845490415.6882599113928.6384279987-7.31386343149
111.706080576320.182434244626-0.9744786080782.32640448166-1.296813077751.48896227869-0.6174672881030.02255224605490.0614691159105-0.4435091874250.2863043034610.3448252177090.776433877455-0.178968638582-1.041017598430.372871335677-0.00826717370618-0.02551089980861.11482712634-0.1943098647671.03075806661-29.452297235326.2782768169-6.38641888194
123.20886698683-0.174049589642-1.395821571050.633859692320.03520784883842.191922400330.08470931221980.1541372907650.093563396009-0.127319445582-0.0430897637958-0.134562285870.130425228682-0.2245236862342.317618539730.442731285069-0.0745612071487-0.02558113849830.231993037613-0.1491168088070.552210757271-3.3239262539123.7916496682-5.42944172994
134.53406017863-1.831150724621.223773850362.676535922610.5432550516640.893830257943-0.345486559835-0.2469029323850.1783563730670.007603625969540.03696178497550.431025788882-0.27406509774-0.02507955512410.2095857740740.492958182929-0.183630006890.04973705786230.4506079982760.03611123726710.644885729001-5.644535919585.6927312539312.9693208384
142.283908167480.903389143681-0.009445249553641.398804864841.482261484611.678576363520.530914645995-1.219082885680.1861968503020.807987216485-0.613563277099-0.1153556780990.156817716050.355450836544-0.1389721114190.554159713414-0.07319507919580.003518969728290.725470312249-0.03456108821270.664003313739-18.986231633113.979638970922.9231555134
152.783193962691.13719578645-0.1686674996011.33453944802-1.38688580211.51183791269-0.0464563197494-0.355593803158-0.6063955602640.0943346045999-0.0221733683292-0.01192929780170.489136963278-0.0970910131194-0.1030877072770.5282372254450.0116000175417-0.02172076875940.38251512254-0.02171944782260.959593496203-3.450835517053.2653107503214.5932020608
163.717506431911.19168290189-0.6459565869423.159103662931.336804497152.065480148930.138142880176-1.355925750990.00153777099790.42612692458-0.4698757156730.6698295553090.37751285738-0.08186959940670.3089194764080.47316601983-0.0361392435920.08987360598050.6388813431120.09491724270141.13836700748-13.20059866345.865605638216.4007091413
172.69572147440.948042760513-0.2873282308711.94818425050.728911552141.300762711040.139293261789-0.4021054062740.001291951336350.138577576289-0.2519828014880.04159843085870.0509582265472-0.100960370980.02046383747790.450491919886-0.04477613755340.02588009161140.446179373555-0.0387913918390.610423669544-3.581913561957.1774082741413.3810592053
184.50038167857-0.6376252658240.8132480446742.63540128557-0.04732217309092.162012929340.06192207023710.275202282488-0.500731014603-0.2414180272390.14945576282-0.001411141211610.1749023498520.325310640362-0.05145092446620.4013120079440.07143813739660.05053773510930.205524666350.03620933063870.425406447889-8.5482909913647.407100979116.8612736372
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 110 through 174 )CC110 - 174110 - 174
22chain 'C' and (resid 175 through 268 )CC175 - 268175 - 255
33chain 'D' and (resid 2 through 30 )DD2 - 301 - 29
44chain 'D' and (resid 31 through 156 )DD31 - 15630 - 147
55chain 'D' and (resid 157 through 182 )DD157 - 182148 - 171
66chain 'D' and (resid 183 through 268 )DD183 - 268172 - 246
77chain 'A' and (resid 2 through 30 )AA2 - 301 - 29
88chain 'A' and (resid 31 through 56 )AA31 - 5630 - 51
99chain 'A' and (resid 57 through 112 )AA57 - 11252 - 100
1010chain 'A' and (resid 113 through 166 )AA113 - 166101 - 154
1111chain 'A' and (resid 167 through 184 )AA167 - 184155 - 172
1212chain 'A' and (resid 185 through 268 )AA185 - 268173 - 250
1313chain 'B' and (resid 1 through 30 )BB1 - 301 - 30
1414chain 'B' and (resid 31 through 55 )BB31 - 5531 - 55
1515chain 'B' and (resid 56 through 99 )BB56 - 9956 - 92
1616chain 'B' and (resid 100 through 154 )BB100 - 15493 - 142
1717chain 'B' and (resid 155 through 268 )BB155 - 268143 - 236
1818chain 'C' and (resid 1 through 109 )CC1 - 1091 - 109

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