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- PDB-8jyv: Crystal structure of the gasdermin from Trichoplax adhaerens -

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Basic information

Entry
Database: PDB / ID: 8jyv
TitleCrystal structure of the gasdermin from Trichoplax adhaerens
ComponentsGasdermin pore forming domain-containing protein
KeywordsIMMUNE SYSTEM / Pyroptosis / Gasdermnin
Function / homologyGasdermin-E / Gasdermin, pore forming domain / Gasdermin pore forming domain / programmed cell death / Gasdermin pore forming domain-containing protein
Function and homology information
Biological speciesTrichoplax adhaerens (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsZeng, H. / Hou, Y.J. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Science / Year: 2024
Title: Cleavage-independent activation of ancient eukaryotic gasdermins and structural mechanisms.
Authors: Yueyue Li / Yanjie Hou / Qi Sun / Huan Zeng / Fanyi Meng / Xiang Tian / Qun He / Feng Shao / Jingjin Ding /
Abstract: Gasdermins (GSDMs) are pore-forming proteins that execute pyroptosis for immune defense. GSDMs are two-domain proteins activated by proteolytic removal of the inhibitory domain. In this work, we ...Gasdermins (GSDMs) are pore-forming proteins that execute pyroptosis for immune defense. GSDMs are two-domain proteins activated by proteolytic removal of the inhibitory domain. In this work, we report two types of cleavage-independent GSDM activation. First, GSDM, a pore-forming domain-only protein from the basal metazoan , is a disulfides-linked autoinhibited dimer activated by reduction of the disulfides. The cryo-electron microscopy (cryo-EM) structure illustrates the assembly mechanism for the 44-mer GSDM pore. Second, RCD-1-1 and RCD-1-2, encoded by the polymorphic () gene in filamentous fungus , are also pore-forming domain-only GSDMs. RCD-1-1 and RCD-1-2, when encountering each other, form pores and cause pyroptosis, underlying allorecognition in . The cryo-EM structure reveals a pore of 11 RCD-1-1/RCD-1-2 heterodimers and a heterodimerization-triggered pore assembly mechanism. This study shows mechanistic diversities in GSDM activation and indicates versatile functions of GSDMs.
History
DepositionJul 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Gasdermin pore forming domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,2471
Polymers26,2471
Non-polymers00
Water1,65792
1
A: Gasdermin pore forming domain-containing protein

A: Gasdermin pore forming domain-containing protein


Theoretical massNumber of molelcules
Total (without water)52,4932
Polymers52,4932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.718, 55.718, 140.085
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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Components

#1: Protein Gasdermin pore forming domain-containing protein


Mass: 26246.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Gene: TRIADDRAFT_52857 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3RMM6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM sodium citrate tribasic dihydrate pH 5.0, 18% polyethylene glycol 3550, 80 mM lithium nitrate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.86→48.25 Å / Num. obs: 21681 / % possible obs: 99.4 % / Redundancy: 18.1 % / Biso Wilson estimate: 38.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.014 / Rrim(I) all: 0.062 / Net I/σ(I): 34.7
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1237 / CC1/2: 0.968 / Rpim(I) all: 0.164 / Rrim(I) all: 0.581 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→33.56 Å / SU ML: 0.2405 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 1988 9.21 %
Rwork0.2142 19596 -
obs0.2161 21584 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.8 Å2
Refinement stepCycle: LAST / Resolution: 1.86→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 92 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641835
X-RAY DIFFRACTIONf_angle_d0.79982485
X-RAY DIFFRACTIONf_chiral_restr0.0508304
X-RAY DIFFRACTIONf_plane_restr0.0074317
X-RAY DIFFRACTIONf_dihedral_angle_d12.9582690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.36251290.30591256X-RAY DIFFRACTION92.58
1.91-1.960.30571360.27771348X-RAY DIFFRACTION97.89
1.96-2.020.31881410.24971361X-RAY DIFFRACTION99.21
2.02-2.090.26781340.22721384X-RAY DIFFRACTION99.54
2.09-2.160.23881440.23841401X-RAY DIFFRACTION99.48
2.16-2.250.27441380.23721390X-RAY DIFFRACTION99.48
2.25-2.350.26561380.26181395X-RAY DIFFRACTION99.8
2.35-2.470.28081420.22341414X-RAY DIFFRACTION100
2.47-2.630.27611410.25631387X-RAY DIFFRACTION99.93
2.63-2.830.29041450.24391421X-RAY DIFFRACTION100
2.83-3.110.2741420.24371427X-RAY DIFFRACTION100
3.11-3.560.24081480.20661420X-RAY DIFFRACTION100
3.56-4.490.19021500.2021450X-RAY DIFFRACTION100
4.49-33.560.19851600.17851542X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 15.7256984202 Å / Origin y: -0.450990440407 Å / Origin z: 3.44676992512 Å
111213212223313233
T0.193596413816 Å20.0210987140809 Å2-0.0160661110558 Å2-0.280815894956 Å2-0.0413381045845 Å2--0.252328204608 Å2
L1.28797918568 °2-0.206264436393 °2-0.262525977217 °2-5.54483968749 °23.00486352855 °2--3.17091194237 °2
S0.132671426267 Å °-0.022873501372 Å °-0.0371871785453 Å °-0.115552642203 Å °-0.0393872099104 Å °-0.0193768227971 Å °-0.0534031683649 Å °0.200067224009 Å °-0.075763232054 Å °
Refinement TLS groupSelection details: all

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