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- PDB-8jyx: Crystal structure of the gasdermin-like protein RCD-1-1 from Neur... -

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Basic information

Entry
Database: PDB / ID: 8jyx
TitleCrystal structure of the gasdermin-like protein RCD-1-1 from Neurospora crassa
ComponentsMaltodextrin-binding protein,Gasdermin-like protein rcd-1-1
KeywordsIMMUNE SYSTEM / Pyroptosis / Gasdermnin / Allorecognition
Function / homology
Function and homology information


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
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Gasdermin-like protein rcd-1-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Neurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLi, Y. / 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 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Gasdermin-like protein rcd-1-1
B: Maltodextrin-binding protein,Gasdermin-like protein rcd-1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,9154
Polymers139,2312
Non-polymers6852
Water2,918162
1
A: Maltodextrin-binding protein,Gasdermin-like protein rcd-1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9582
Polymers69,6151
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltodextrin-binding protein,Gasdermin-like protein rcd-1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9582
Polymers69,6151
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.144, 91.911, 105.868
Angle α, β, γ (deg.)90.000, 101.380, 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 Maltodextrin-binding protein,Gasdermin-like protein rcd-1-1 / Regulator of cell death 1-1


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.) Escherichia coli (E. coli), (gene. exp.) Neurospora crassa (fungus)
Gene: malE, NCTC8450_00456, NCTC9775_03059, rcd-1-1, NCU05712
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A376KDN7, UniProt: Q7SBA0
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.78 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.96 Å / SU ML: 0.3492 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 2000 3.15 %
Rwork0.2165 61475 -
obs0.2175 63475 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.05 Å2
Refinement stepCycle: LAST / Resolution: 2.35→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8741 0 46 162 8949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219010
X-RAY DIFFRACTIONf_angle_d0.460212220
X-RAY DIFFRACTIONf_chiral_restr0.18261328
X-RAY DIFFRACTIONf_plane_restr0.00311559
X-RAY DIFFRACTIONf_dihedral_angle_d11.35353280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.39981420.32734362X-RAY DIFFRACTION99.78
2.41-2.470.36531410.31454350X-RAY DIFFRACTION99.76
2.47-2.550.3951440.30194394X-RAY DIFFRACTION99.71
2.55-2.630.35061410.28964342X-RAY DIFFRACTION99.78
2.63-2.720.35441420.27814365X-RAY DIFFRACTION99.91
2.72-2.830.27211420.2544369X-RAY DIFFRACTION99.91
2.83-2.960.26061440.2494410X-RAY DIFFRACTION99.91
2.96-3.120.25751430.24664402X-RAY DIFFRACTION99.87
3.12-3.310.27991420.25244378X-RAY DIFFRACTION99.96
3.31-3.570.2561430.22654379X-RAY DIFFRACTION100
3.57-3.930.26571420.22754390X-RAY DIFFRACTION99.26
3.93-4.490.21221440.18174411X-RAY DIFFRACTION99.87
4.49-5.660.20311440.16544437X-RAY DIFFRACTION99.96
5.66-45.960.1791460.16684486X-RAY DIFFRACTION99.04

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