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- PDB-7z1x: Crystal structure of human Gasdermin D complexed with nanobodies ... -

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Basic information

Entry
Database: PDB / ID: 7z1x
TitleCrystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6
Components
  • Gasdermin-D
  • VHH-2
  • VHH-6
KeywordsIMMUNE SYSTEM / Gasdermin D / GSDMD / nanobody / VHH / inflammation / pyroptosis
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 / ficolin-1-rich granule lumen / defense response to Gram-negative bacterium / 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)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKopp, A. / Hagelueken, G. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)IRTG 2168 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Pyroptosis inhibiting nanobodies block Gasdermin D pore formation.
Authors: Kopp, A. / Hagelueken, G. / Jamitzky, I. / Moecking, J. / Schiffelers, L.D.J. / Schmidt, F.I. / Geyer, M.
History
DepositionFeb 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gasdermin-D
B: VHH-2
C: VHH-6
D: Gasdermin-D
E: VHH-2
F: VHH-6


Theoretical massNumber of molelcules
Total (without water)157,3906
Polymers157,3906
Non-polymers00
Water10,034557
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.353, 108.353, 124.041
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 48818.133 Da / Num. of mol.: 2
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
#2: Antibody VHH-2


Mass: 14457.917 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody VHH-6


Mass: 15419.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 20 mg/ml protein complex; 0.04 M NaCl, 25.8% (v/v) PEG400, 0.05 M Na3Cit pH 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976255 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976255 Å / Relative weight: 1
ReflectionResolution: 1.86→93.84 Å / Num. obs: 136585 / % possible obs: 99.66 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.0163 / Rpim(I) all: 0.0163 / Rrim(I) all: 0.02305 / Net I/σ(I): 17.43
Reflection shellResolution: 1.86→1.926 Å / Rmerge(I) obs: 0.8545 / Mean I/σ(I) obs: 0.73 / Num. unique obs: 13351 / CC1/2: 0.443 / Rpim(I) all: 0.8545

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Processing

Software
NameVersionClassification
PHENIX(1.20_4444: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N9O, 5IVO

6n9o

5ivo


Resolution: 1.86→93.84 Å / Cross valid method: FREE R-VALUE / σ(F): 78.45 / Phase error: 31.31 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2494 4016 1.48 %
Rwork0.2124 --
obs0.2238 136585 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→93.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9660 0 0 557 10217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.774
X-RAY DIFFRACTIONf_dihedral_angle_d5.7251352
X-RAY DIFFRACTIONf_chiral_restr0.0451527
X-RAY DIFFRACTIONf_plane_restr0.0081751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.890.28761610.308311140X-RAY DIFFRACTION81
1.89-1.930.32592080.310813390X-RAY DIFFRACTION98
1.93-1.960.34891920.316913587X-RAY DIFFRACTION99
1.96-20.31041960.316313501X-RAY DIFFRACTION99
2-2.050.3772000.313613580X-RAY DIFFRACTION99
2.05-2.090.29452080.323413316X-RAY DIFFRACTION98
2.09-2.150.33922000.318313537X-RAY DIFFRACTION99
2.15-2.20.30192120.32413647X-RAY DIFFRACTION98
2.2-2.270.31721920.317613398X-RAY DIFFRACTION99
2.27-2.340.30542000.321213520X-RAY DIFFRACTION99
2.34-2.430.28972080.318413614X-RAY DIFFRACTION98
2.43-2.520.30682080.313113484X-RAY DIFFRACTION98
2.52-2.640.31191880.29813487X-RAY DIFFRACTION99
2.64-2.780.32592080.277913512X-RAY DIFFRACTION98
2.78-2.950.29931800.268713518X-RAY DIFFRACTION99
2.95-3.180.28232040.240913546X-RAY DIFFRACTION99
3.18-3.50.23822000.217413497X-RAY DIFFRACTION99
3.5-40.23732000.182513580X-RAY DIFFRACTION99
4-5.040.18471960.14413388X-RAY DIFFRACTION99
5.05-93.840.25322240.180213503X-RAY DIFFRACTION98

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