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- PDB-8jyx: Crystal structure of the gasdermin-like protein RCD-1-1 from Neur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jyx | ||||||
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Title | Crystal structure of the gasdermin-like protein RCD-1-1 from Neurospora crassa | ||||||
![]() | Maltodextrin-binding protein,Gasdermin-like protein rcd-1-1 | ||||||
![]() | IMMUNE SYSTEM / Pyroptosis / Gasdermnin / Allorecognition | ||||||
Function / homology | ![]() wide pore channel activity / programmed cell death / carbohydrate transmembrane transporter activity / outer membrane-bounded periplasmic space / protein heterodimerization activity / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, Y. / Hou, Y.J. / Ding, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.7 KB | Display | ![]() |
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PDB format | ![]() | 184.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jyvC ![]() 8jywC ![]() 8jyyC ![]() 8jyzC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 69615.359 Da / Num. of mol.: 2 Mutation: D108A, K109A, E198A, N199A, K265A, K388A, D389A, K174A, K175A, K176A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: malE, NCTC8450_00456, NCTC9775_03059, rcd-1-1, NCU05712 Production host: ![]() ![]() #2: Polysaccharide | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.1 M Bicine pH 7.4, 11% PEG 3350, 3% (w/v) D(+)-Glucose monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→79.55 Å / Num. obs: 63588 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 45.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.098 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4459 / CC1/2: 0.881 / Rpim(I) all: 0.465 / Rrim(I) all: 0.886 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→45.96 Å
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Refine LS restraints |
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LS refinement shell |
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