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- PDB-9hjp: Improved structure of mouse Gasdermin D -

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Basic information

Entry
Database: PDB / ID: 9hjp
TitleImproved structure of mouse Gasdermin D
ComponentsGasdermin-D
KeywordsIMMUNE SYSTEM / Inflammatory response
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / pyroptotic cell death / Regulation of TLR by endogenous ligand / Interleukin-1 processing / pore complex assembly / wide pore channel activity / NLRP3 inflammasome complex / phosphatidic acid binding / cardiolipin binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / pyroptotic cell death / Regulation of TLR by endogenous ligand / Interleukin-1 processing / pore complex assembly / wide pore channel activity / NLRP3 inflammasome complex / phosphatidic acid binding / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / protein secretion / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / positive regulation of interleukin-1 beta production / mitochondrial membrane / protein homooligomerization / positive regulation of inflammatory response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / extracellular space / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Gasdermin-D
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.636 Å
AuthorsDe Colibus, L. / Biasutto, A. / Jazayeri, A. / Duerr, K.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateNA United Kingdom
CitationJournal: To Be Published
Title: Improved structure of mouse Gasdermin D
Authors: De Colibus, L. / Biasutto, A. / Jazayeri, A. / Duerr, K.L.
History
DepositionNov 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gasdermin-D
B: Gasdermin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8559
Polymers99,3092
Non-polymers5467
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-54 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.209, 86.934, 82.466
Angle α, β, γ (deg.)90, 95.24, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 49654.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Differences with the WT sequence are reported below. Deleted residues: S182-L187, E196-G199, R248-L279
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmd, Gsdmdc1 / Production host: Escherichia coli 0.1288 (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D8T2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 27%PEG3350, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.636→82.121 Å / Num. obs: 16610 / % possible obs: 92.3 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rpim(I) all: 0.056 / Net I/σ(I): 11.3
Reflection shellResolution: 2.636→2.958 Å / Redundancy: 12 % / Num. unique obs: 830 / CC1/2: 0.679 / % possible all: 68.7

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.636→33.95 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 781 -RANDOM
Rwork0.2386 ---
obs0.2396 16596 59.1 %-
Displacement parametersBiso mean: 89.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.9516 Å20 Å2-9.5483 Å2
2--3.6975 Å20 Å2
3----1.7459 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.636→33.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6158 0 17 42 6217
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0066277HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.888505HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2228SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1042HARMONIC5
X-RAY DIFFRACTIONt_it6277HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion817SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4493SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion17.32
LS refinement shellResolution: 2.64→2.85 Å
RfactorNum. reflection% reflection
Rfree0.3601 15 -
Rwork0.2958 --
obs0.298 426 7.17 %
Refinement TLS params.

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)
125.54374.8259-2.904518.1594.503917.2651-0.2315-0.94880.1796-0.94880.16981.73090.17961.73090.0617-0.2189-0.09520.00620.5105-0.0862-0.006611.31738.0638.9829
211.2298-4.0191-1.428914.33925.227314.4631-0.2058-0.2689-0.1642-0.2689-0.0136-0.908-0.1642-0.9080.2194-0.5425-0.1208-0.1769-0.10880.1304-0.359-5.82463.690133.2498
319.74558.37095.717513.43524.32810.75420.04490.793-0.01110.793-0.3398-0.8065-0.0111-0.80650.2949-0.12130.38370.0135-0.10270.2678-0.4589-4.05087.282245.4512
45.1079-1.139-0.23550-1.04015.6743-0.0474-0.3274-1.1384-0.3274-0.06880.5813-1.13840.58130.1162-0.0186-0.0283-0.0518-0.08960.0684-0.02866.937413.52830.6502
53.85790.1748-0.23513.7020.87135.4542-0.2548-0.73760.9225-0.73760.1989-0.22430.9225-0.22430.05590.0518-0.12960.00160.09630.02330.30271.3174-4.211419.9431
617.03561.62514.28827.70942.204211.63450.0727-0.54030.829-0.54030.1681.03470.8291.0347-0.2408-0.00390.02150.2583-0.2163-0.10040.560316.4015-5.904519.994
725.42444.089-2.396814.7632-4.102420.38040.51840.96590.48940.9659-0.85721.5250.48941.5250.3388-0.50870.1167-0.0037-0.260.2730.632122.235-2.555326.8421
89.8704-0.07762.762810.4443-0.12443.14140.45140.3430.44640.343-0.3256-0.62540.4464-0.6254-0.1258-0.1759-0.1119-0.1045-0.1410.0194-0.328515.0894-3.335567.7536
92.68040.14630.698510.420.67023.27490.1115-0.0626-0.2902-0.0626-0.12210.1605-0.29020.16050.0106-0.1352-0.0804-0.1046-0.08060.0888-0.577820.9921-0.387165.7233
1011.39341.53116.3665.35881.63478.7628-0.206-0.1734-0.0394-0.1734-0.0476-0.1415-0.0394-0.14150.2536-0.26510.1141-0.0786-0.4543-0.0252-0.352915.9901-24.403169.8779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 30}
2X-RAY DIFFRACTION2{A|31 -75}
3X-RAY DIFFRACTION3{A|76 - 145}
4X-RAY DIFFRACTION4{A|146 - 209}
5X-RAY DIFFRACTION5{A|210 - 359}
6X-RAY DIFFRACTION6{A|360 - 434}
7X-RAY DIFFRACTION7{A|435 - 483}
8X-RAY DIFFRACTION8{B|1 - 65}
9X-RAY DIFFRACTION9{B|66 - 307}
10X-RAY DIFFRACTION10{B|308 - 503}

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