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- PDB-6ao4: Crystal structure of the human gasdermin D C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6ao4
TitleCrystal structure of the human gasdermin D C-terminal domain
ComponentsGasdermin-D
KeywordsIMMUNE SYSTEM / Inflammasome / pyroptosis / gasdermin D / autoinhibition / Salmonella infection
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 / pyroptotic inflammatory response / 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, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsLiu, Z. / Wang, C. / Yang, J. / Xiao, T.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR069908 United States
CitationJournal: Structure / Year: 2018
Title: Structures of the Gasdermin D C-Terminal Domains Reveal Mechanisms of Autoinhibition.
Authors: Liu, Z. / Wang, C. / Rathkey, J.K. / Yang, J. / Dubyak, G.R. / Abbott, D.W. / Xiao, T.S.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)22,3541
Polymers22,3541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.750, 108.540, 45.910
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: 22354.439 Da / Num. of mol.: 1 / Fragment: unp residues 277-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMD, DFNA5L, GSDMDC1, FKSG10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus RIPL / References: UniProt: P57764

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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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M DL-malic acid, pH 7.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→42.3 Å / Num. obs: 5664 / % possible obs: 99.9 % / Redundancy: 6.67 % / CC1/2: 0.998 / Net I/σ(I): 17.5
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 7.19 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 402 / CC1/2: 0.865 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AO3

6ao3


Resolution: 2.901→35.05 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 39.29
RfactorNum. reflection% reflection
Rfree0.2897 367 6.49 %
Rwork0.2321 --
obs0.236 5654 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.901→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 0 0 1445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081468
X-RAY DIFFRACTIONf_angle_d1.1951999
X-RAY DIFFRACTIONf_dihedral_angle_d19.672895
X-RAY DIFFRACTIONf_chiral_restr0.048240
X-RAY DIFFRACTIONf_plane_restr0.008258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9006-3.320.4011230.28451704X-RAY DIFFRACTION100
3.32-4.18180.27971240.26181746X-RAY DIFFRACTION100
4.1818-35.0530.27341200.20941837X-RAY DIFFRACTION100
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)
13.0787-1.237-0.14866.49441.61653.00020.1118-0.422-0.06780.892-0.06990.328-1.18840.02760.12880.8752-0.05960.06510.641-0.43061.180518.478638.451825.9148
22.3558-0.7338-1.26376.5482-0.55315.4856-0.10271.5971-0.6726-0.66440.17950.20060.3865-0.1745-0.06080.8276-0.1660.17131.0944-0.3420.775619.94938.93635.018
32.22861.46640.16622.41612.43163.59410.26230.71140.5592-0.13610.36450.1026-0.38580.39010.03891.3354-0.38091.22072.1014-0.72010.748433.004842.98361.9834
43.16090.4664-0.52454.664-3.04172.43570.19861.0514-0.2131-0.353-0.4447-0.5181-0.00840.67920.07180.784-0.22590.14261.122-0.4710.661523.138437.70898.6301
55.42981.21412.47857.9803-1.42817.5387-0.1964-0.87470.39451.58650.37880.61190.2492-0.2914-0.3630.79270.12890.10870.6465-0.19870.759413.783125.474725.9063
64.5143-2.2189-0.22487.40671.66333.54150.0170.3365-1.7019-0.43760.15970.26820.48110.0435-0.23450.79420.04940.21980.6035-0.27351.469411.904416.496420.1853
75.0079-2.0854-1.38148.3154-0.36734.2126-1.30430.0782-0.74630.74571.5955-0.4922-0.3434-0.024-0.25340.6056-0.13840.09220.9006-0.4120.848518.202530.78518.8914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 284 through 300 )
2X-RAY DIFFRACTION2chain 'A' and (resid 301 through 330 )
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 346 )
4X-RAY DIFFRACTION4chain 'A' and (resid 347 through 395 )
5X-RAY DIFFRACTION5chain 'A' and (resid 396 through 421 )
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 459 )
7X-RAY DIFFRACTION7chain 'A' and (resid 460 through 481 )

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