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- PDB-9e0v: GSDMD bound to a peptide -

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Basic information

Entry
Database: PDB / ID: 9e0v
TitleGSDMD bound to a peptide
Components
  • GLY-CYS-ILE-LYS-LYS-ALA-VAL-6CW-PHE-LYS-CYS
  • Maltose/maltodextrin-binding periplasmic protein, Gasdermin-D, C-terminal chimera
KeywordsIMMUNE SYSTEM / GSDMD / Caspase / exosite / pyroptosis / cyclic peptide / druggability
Function / homology
Function and homology information


pyroptotic cell death / pore complex assembly / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / Regulation of TLR by endogenous ligand / phosphatidic acid binding / Interleukin-1 processing / cardiolipin binding / phosphatidylinositol-4-phosphate binding ...pyroptotic cell death / pore complex assembly / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / Regulation of TLR by endogenous ligand / phosphatidic acid binding / Interleukin-1 processing / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / detection of maltose stimulus / maltose transport complex / carbohydrate transport / protein secretion / carbohydrate transmembrane transporter activity / maltose binding / Pyroptosis / maltose transport / maltodextrin transmembrane transport / Purinergic signaling in leishmaniasis infection / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / phosphatidylinositol-4,5-bisphosphate binding / ATP-binding cassette (ABC) transporter complex / positive regulation of interleukin-1 beta production / cell chemotaxis / protein homooligomerization / mitochondrial membrane / specific granule lumen / positive regulation of inflammatory response / tertiary granule lumen / outer membrane-bounded periplasmic space / defense response to Gram-negative bacterium / ficolin-1-rich granule lumen / periplasmic space / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / DNA damage response / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Gasdermin-D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.635 Å
AuthorsWang, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Peptide binding at the Gasdermin D exosite reveals structural basis for targeting the site
Authors: Wang, R.
History
DepositionOct 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein, Gasdermin-D, C-terminal chimera
B: GLY-CYS-ILE-LYS-LYS-ALA-VAL-6CW-PHE-LYS-CYS


Theoretical massNumber of molelcules
Total (without water)65,4192
Polymers65,4192
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: nanoDSF for Tm shift
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-10 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.575, 47.575, 194.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein, Gasdermin-D, C-terminal chimera / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / GSDMD-CT / hGSDMD-CTD


Mass: 64098.516 Da / Num. of mol.: 1 / Fragment: MBP + GSD (UNP residues 276-484)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: malE, b4034, JW3994, GSDMD, DFNA5L, GSDMDC1, FKSG10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: P57764
#2: Protein/peptide GLY-CYS-ILE-LYS-LYS-ALA-VAL-6CW-PHE-LYS-CYS


Mass: 1320.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 1.25 M sodium citrate dihydrate, 20 mM TCEP

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Data collection

DiffractionMean temperature: 103.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00000 A
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.629→48.68 Å / Num. obs: 28835 / % possible obs: 89.3 % / Redundancy: 11.8 % / CC1/2: 0.99 / Rrim(I) all: 0.053 / Net I/σ(I): 25.9
Reflection shellResolution: 1.629→1.629 Å / Num. unique obs: 26002 / CC1/2: 0.7 / Rrim(I) all: 0.68

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (10-JUL-2024)refinement
pointlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.635→19.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 1268 4.91 %RANDOM
Rwork0.2003 ---
obs0.2009 25817 89.6 %-
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.2404 Å20 Å20 Å2
2---0.2404 Å20 Å2
3---0.4807 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.635→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 15 141 1756
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011647HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12241HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d567SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes278HARMONIC5
X-RAY DIFFRACTIONt_it1647HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion14.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion205SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1707SEMIHARMONIC4
LS refinement shellResolution: 1.64→1.65 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3456 -4.84 %
Rwork0.2816 492 -
all0.2845 517 -
obs--58.33 %

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