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- PDB-8jyy: Crystal structure of the gasdermin-like protein RCD-1-2 from Neur... -

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Basic information

Entry
Database: PDB / ID: 8jyy
TitleCrystal structure of the gasdermin-like protein RCD-1-2 from Neurospora crassa
ComponentsRCD-1-2
KeywordsIMMUNE SYSTEM / Pyroptosis / Gasdermnin / Allorecognition
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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. Here we report two ...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. Here 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. Cryo-electron microscopy (cryo-EM) structure illustrates assembly mechanism for the 44-mer GSDM pore. Second, RCD-1-1/RCD-1-2, encoded by polymorphic 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 . Cryo-EM structure reveals a pore of 11 RCD-1-1/RCD-1-2 heterodimers and 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RCD-1-2
B: RCD-1-2
C: RCD-1-2
D: RCD-1-2
E: RCD-1-2
F: RCD-1-2
G: RCD-1-2
H: RCD-1-2
I: RCD-1-2
J: RCD-1-2


Theoretical massNumber of molelcules
Total (without water)243,47610
Polymers243,47610
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27200 Å2
ΔGint-133 kcal/mol
Surface area78050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.550, 146.706, 126.076
Angle α, β, γ (deg.)90.000, 104.570, 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
RCD-1-2


Mass: 24347.625 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: rcd-1-2 / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 49.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8 M succinic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→48.9 Å / Num. obs: 66913 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 47.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.052 / Rrim(I) all: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4503 / CC1/2: 0.773 / Rpim(I) all: 0.374 / Rrim(I) all: 0.882 / % 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: 2.65→48.39 Å / SU ML: 0.3924 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 2007 3.01 %
Rwork0.2186 64754 -
obs0.22 66761 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.19 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14381 0 0 0 14381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214797
X-RAY DIFFRACTIONf_angle_d0.455920099
X-RAY DIFFRACTIONf_chiral_restr0.04282159
X-RAY DIFFRACTIONf_plane_restr0.00362573
X-RAY DIFFRACTIONf_dihedral_angle_d11.58895397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.33751450.2964630X-RAY DIFFRACTION99.96
2.72-2.790.34711380.28634587X-RAY DIFFRACTION99.98
2.79-2.870.37841410.29284664X-RAY DIFFRACTION99.98
2.87-2.960.37191380.29024607X-RAY DIFFRACTION100
2.96-3.070.36181460.27494627X-RAY DIFFRACTION100
3.07-3.190.32671400.25414600X-RAY DIFFRACTION99.96
3.19-3.340.31291480.26054645X-RAY DIFFRACTION99.98
3.34-3.510.32181420.24884628X-RAY DIFFRACTION99.92
3.51-3.730.33511400.2484500X-RAY DIFFRACTION97.48
3.73-4.020.2441450.21514637X-RAY DIFFRACTION100
4.02-4.430.21191470.184624X-RAY DIFFRACTION99.98
4.43-5.070.20431480.1644664X-RAY DIFFRACTION99.92
5.07-6.380.21281450.19174636X-RAY DIFFRACTION99.83
6.38-48.390.19691440.17684705X-RAY DIFFRACTION99.55

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