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- PDB-5nh1: Structure of the C-terminal domain of human Gasdermin D -

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Basic information

Entry
Database: PDB / ID: 5nh1
TitleStructure of the C-terminal domain of human Gasdermin D
ComponentsGasdermin-D
KeywordsIMMUNE SYSTEM / apoptosis / Gasdermin / pyroptosis / inflammasome / innate immunity
Function / homology
Function and homology information


pore complex assembly / : / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / cardiolipin binding / Regulation of TLR by endogenous ligand / phosphatidic acid binding / Interleukin-1 processing / phosphatidylinositol-4-phosphate binding ...pore complex assembly / : / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / cardiolipin binding / Regulation of TLR by endogenous ligand / phosphatidic acid binding / Interleukin-1 processing / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptosis / protein secretion / Pyroptosis / Purinergic signaling in leishmaniasis infection / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / mitochondrial membrane / protein homooligomerization / positive regulation of inflammatory response / specific granule lumen / tertiary granule lumen / defense response to Gram-negative bacterium / ficolin-1-rich granule lumen / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Gasdermin / Gasdermin, pore forming domain / Gasdermin pore forming domain / Gasdermin, PUB domain / Gasdermin PUB domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsAnton, L. / Sborgi, L. / Hiller, S. / Broz, P. / Maier, T.
CitationJournal: Biorxiv / Year: 2017
Title: Insights into Gasdermin D activation from the crystal structure of its C-terminal domain
Authors: Anton, L. / Sborgi, L. / Hiller, S. / Broz, P. / Maier, T.
History
DepositionMar 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)22,1681
Polymers22,1681
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.730, 47.980, 37.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22168.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMD, DFNA5L, GSDMDC1, FKSG10 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P57764
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / Details: 1.229 M NaCitrate, HEPES, pH 7.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.04→44.827 Å / Num. obs: 14421 / % possible obs: 95 % / Redundancy: 8.4 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.196 / Net I/σ(I): 8.63
Reflection shellResolution: 2.04→2.16 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2240 / CC1/2: 0.717 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2131: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5R

5b5r


Resolution: 2.04→44.827 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 749 5.19 %
Rwork0.2311 --
obs0.2328 14419 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→44.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 0 161 1653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021521
X-RAY DIFFRACTIONf_angle_d0.5532074
X-RAY DIFFRACTIONf_dihedral_angle_d14.797926
X-RAY DIFFRACTIONf_chiral_restr0.033247
X-RAY DIFFRACTIONf_plane_restr0.003270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0402-2.19770.37411590.29352715X-RAY DIFFRACTION97
2.1977-2.41890.28551360.26542748X-RAY DIFFRACTION97
2.4189-2.76880.29361530.26572726X-RAY DIFFRACTION96
2.7688-3.48820.24061460.22772711X-RAY DIFFRACTION94
3.4882-44.83770.23531550.19662770X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / 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)
19.46630.40233.62914.32190.65158.08960.5107-0.7798-0.06420.58360.05240.09010.1679-0.5865-0.32170.51240.0150.04270.28260.00730.221224.4492119.294327.0276
22.12651.3382.79545.18982.12165.97740.1453-0.5575-0.80060.2474-0.21950.56530.2459-1.11040.00030.35370.03810.00630.44770.11050.467111.7517112.961210.07
37.501-3.3683-3.18792.12912.70374.85070.11270.11391.6738-0.2056-0.0226-0.4286-0.64280.772-0.230.3583-0.0460.06330.29960.02940.304919.2793126.77032.7913
43.97680.4764-0.33082.12840.47242.62350.5143-0.92811.3524-0.1268-0.15060.7111-0.692-0.86850.13180.5365-0.1288-0.0470.775-0.10090.59258.0195131.30266.9444
56.63711.41122.28291.6282-0.03783.44020.213-0.7270.2926-0.0361-0.22370.18460.3424-0.70390.10130.2934-0.03150.01270.3437-0.02960.207511.2521123.4089.5406
68.2732.51350.29226.3795-1.78843.195-0.24140.6729-0.1883-0.31710.2938-0.17680.2253-0.0266-0.0040.28980.0105-0.00730.20490.03180.151227.267115.80714.6562
72.7329-0.93130.40652.6651-0.49792.083-0.0041-0.10160.0053-0.04540.0066-0.23760.16620.1059-0.04150.24220.00820.01880.1302-0.00250.16635.349112.743216.5782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 282 through 298 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 333 )
4X-RAY DIFFRACTION4chain 'A' and (resid 334 through 346 )
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 380 )
6X-RAY DIFFRACTION6chain 'A' and (resid 381 through 394 )
7X-RAY DIFFRACTION7chain 'A' and (resid 395 through 480 )

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