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- PDB-6n9o: Crystal structure of human GSDMD -

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Basic information

Entry
Database: PDB / ID: 6n9o
TitleCrystal structure of human GSDMD
ComponentsGasdermin-D
KeywordsIMMUNE SYSTEM / Pyroptosis / gasdermin D / inflammasome / autoinhibition
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, 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: 3.5 Å
AuthorsLiu, Z. / Wang, C. / Yang, J. / Xiao, T.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)GM127609 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR069908 United States
CitationJournal: Immunity / Year: 2019
Title: Crystal Structures of the Full-Length Murine and Human Gasdermin D Reveal Mechanisms of Autoinhibition, Lipid Binding, and Oligomerization.
Authors: Liu, Z. / Wang, C. / Yang, J. / Zhou, B. / Yang, R. / Ramachandran, R. / Abbott, D.W. / Xiao, T.S.
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Gasdermin-D
B: Gasdermin-D
C: Gasdermin-D
D: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)211,9804
Polymers211,9804
Non-polymers00
Water0
1
A: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)52,9951
Polymers52,9951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)52,9951
Polymers52,9951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)52,9951
Polymers52,9951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)52,9951
Polymers52,9951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.640, 105.550, 151.790
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 52994.961 Da / Num. of mol.: 4
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) / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.5→49.5 Å / Num. obs: 23251 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 153.7 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.086 / Net I/σ(I): 10.2
Reflection shellResolution: 3.5→3.6 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1695 / CC1/2: 0.605 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3260: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5R, 6AO3, 6AO4

5b5r

6ao3

6ao4


Resolution: 3.5→49.483 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 45.03
RfactorNum. reflection% reflection
Rfree0.3454 1115 4.8 %
Rwork0.2763 --
obs0.2796 23223 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→49.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11601 0 0 0 11601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411809
X-RAY DIFFRACTIONf_angle_d0.89116050
X-RAY DIFFRACTIONf_dihedral_angle_d17.9637167
X-RAY DIFFRACTIONf_chiral_restr0.0471878
X-RAY DIFFRACTIONf_plane_restr0.0052072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.65940.42661430.40212792X-RAY DIFFRACTION99
3.6594-3.85220.4871340.39212704X-RAY DIFFRACTION99
3.8522-4.09350.4821490.38692699X-RAY DIFFRACTION99
4.0935-4.40930.36091570.31182753X-RAY DIFFRACTION99
4.4093-4.85270.36071390.29942783X-RAY DIFFRACTION100
4.8527-5.55410.40411590.28992741X-RAY DIFFRACTION100
5.5541-6.99450.44161030.32772827X-RAY DIFFRACTION99
6.9945-49.48760.25431310.19912809X-RAY DIFFRACTION98
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)
12.89050.81383.9341-2.5297-1.4762-0.6219-0.27880.60780.64470.64040.24060.0690.17360.2678-0.04080.872-0.05780.09310.7273-0.13140.988616.6291-38.0854-24.702
21.8256-2.5891.11591.52510.77163.3183-0.04381.30970.4849-0.46470.1106-0.1989-0.3729-0.0731-0.00011.1835-0.17670.03861.54450.0151.122534.5494-21.2268-39.8321
34.36633.27270.20541.64641.7256-0.02840.5623-0.23740.2815-0.4355-0.67490.30180.48430.5987-0.01481.1038-0.2230.12191.1427-0.05741.208522.3545-10.2887-23.6102
42.48391.64913.89621.5281-0.6113-0.26980.5439-1.08150.6088-0.4691-0.2995-0.37760.43361.33590.11490.9060.48760.10681.1930.09611.032512.3366-36.477.8056
52.7964-2.43320.5171-0.6564-3.8090.3968-0.6217-0.4637-0.3015-0.39240.5666-0.4655-0.7810.77680.07351.24830.4016-0.16891.50460.18331.02092.167-27.757683.627
60.54342.2131-1.01152.3826-2.60570.03810.3113-0.04850.0704-0.57750.60390.11150.54730.56160.0121.5093-0.0451-0.00691.96630.25511.22362.6378-13.681587.6712
7-0.0484-0.206-0.34310.4324-0.97840.99451.8193-0.2549-0.2573-0.8392-0.49470.62531.07770.29660.18910.97340.12670.20541.54790.00171.244717.9265-26.421251.7958
80.24322.27030.96480.72372.5927-0.1569-1.40110.8110.7752-0.63251.28420.3019-0.62461.13590.00561.2843-0.3787-0.02091.92220.0181.202816.7647-9.919249.3883
9-1.2876-0.84640.73930.5486-0.3243-1.06540.3541-0.8406-0.25962.1977-1.95671.1715-0.60583.6164-0.05772.102-0.4482-0.79552.2381-0.24091.634923.7654-7.663956.7743
10-0.3508-1.3981-0.36470.2399-0.47240.5611-0.3074-0.0097-0.26110.2877-0.08820.1854-0.77432.1394-0.03361.34240.0751-0.15481.95220.50061.429720.0674-15.754949.4887
111.2612-1.22820.04830.6879-0.03821.1507-1.9389-3.79571.4687-0.43780.13370.16750.9187-0.3494-0.27661.2183-0.53610.01930.5815-0.1021.42725.1551-5.086655.1734
120.8068-0.61930.602-0.294-0.11421.22310.23530.0053-0.4441-0.71640.33320.5275-0.0194-0.52360.00011.4041-0.1576-0.03241.21860.22421.1974-10.2209-23.713236.7303
130.48180.5454-0.43450.8641-0.58910.95630.0199-1.8631-1.1902-1.26980.7190.69060.1132-0.55210.00031.21390.1982-0.08991.5840.17431.00910.3281-13.949628.1607
141.26341.4028-1.18022.84113.13068.3652-0.940.6113-1.01133.6982.26190.47323.06192.64130.6198-0.4379-0.53560.63920.80170.54151.0534-0.7621-25.771137.1406
151.01680.4864-1.23981.2748-0.34610.835-0.0831-3.1865-2.06971.17421.94591.6657-0.1259-0.09180.0021.44970.2042-0.30770.00930.5881.7535-4.2062-34.787853.6233
161.41222.1711.14841.70190.22220.7274-0.0521-0.6232-0.5766-2.5598-0.19690.7045-0.1421-0.89040.00021.12930.0983-0.0381.08440.21761.23850.3297-36.700848.2384
172.1611.7347-0.69362.04962.15821.8475-0.4018-0.22810.0513-0.4110.15930.0454-0.4410.0736-0.00430.92880.1605-0.04790.4503-0.08370.91989.4316-19.81733.7296
18-0.3641-1.1085-0.9994-0.87970.97092.99670.1119-0.4567-0.16890.2195-0.6269-0.02690.49440.1233-0.00370.75530.09420.00560.9772-0.07011.060624.674-36.24215.1885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 2 through 286 )
2X-RAY DIFFRACTION2chain 'D' and (resid 287 through 380 )
3X-RAY DIFFRACTION3chain 'D' and (resid 381 through 480 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 146 )
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 320 )
6X-RAY DIFFRACTION6chain 'A' and (resid 321 through 480 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 36 )
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 88 )
9X-RAY DIFFRACTION9chain 'B' and (resid 89 through 146 )
10X-RAY DIFFRACTION10chain 'B' and (resid 147 through 223 )
11X-RAY DIFFRACTION11chain 'B' and (resid 224 through 286 )
12X-RAY DIFFRACTION12chain 'B' and (resid 287 through 321 )
13X-RAY DIFFRACTION13chain 'B' and (resid 322 through 364 )
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 395 )
15X-RAY DIFFRACTION15chain 'B' and (resid 396 through 424 )
16X-RAY DIFFRACTION16chain 'B' and (resid 425 through 481 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 286 )
18X-RAY DIFFRACTION18chain 'C' and (resid 287 through 480 )

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