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6vfe

Gasdermin D pore

Method: ELECTRON MICROSCOPY Dmax: 345.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Gasdermin-D, N-terminal

Homo sapiens

UniProt P57764

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 33 PDB declaration: 33-meric（33） Consistent with protein copy count Chain A； UniProt 1–241 Chain B； UniProt 1–241 Chain C； UniProt 1–241 Chain D； UniProt 1–241 Chain E； UniProt 1–241 Chain F； UniProt 1–241 Chain G； UniProt 1–241 Chain H； UniProt 1–241 Chain I； UniProt 1–241 Chain J； UniProt 1–241 Chain K； UniProt 1–241 Chain L； UniProt 1–241 Chain M； UniProt 1–241 Chain N； UniProt 1–241 Chain O； UniProt 1–241 Chain P； UniProt 1–241 Chain Q； UniProt 1–241 Chain R； UniProt 1–241 Chain S； UniProt 1–241 Chain T； UniProt 1–241 Chain U； UniProt 1–241 Chain V； UniProt 1–241 Chain W； UniProt 1–241 Chain X； UniProt 1–241 Chain Y； UniProt 1–241 Chain Z； UniProt 1–241 Chain a； UniProt 1–241 Chain b； UniProt 1–241 Chain c； UniProt 1–241 Chain d； UniProt 1–241 Chain e； UniProt 1–241 Chain f； UniProt 1–241 Chain g； UniProt 1–241 Mutation：L192E No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6VFE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5NH1 Structure of the C-terminal domain of human Gasdermin D Deposited 2017-03-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 278–484（207 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；303 K；1.229 M NaCitrate, HEPES, pH 7.25
Resolution 2.04 Å R-free 0.264
5WQT Structure of a protein involved in pyroptosis Deposited 2016-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 276–484（209 aa） Fragment：C-terminal (UNP RESIDUES 276-484)
Chain B 276–484（209 aa） Fragment：C-terminal (UNP RESIDUES 276-484)
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 3 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；291 K；20mM Sodium bromide, 0.1M Hepes sodium pH7.0, 1.5M Sodium citrate tribasic dihydrate
Resolution 2.64 Å R-free 0.286
6AO4 Crystal structure of the human gasdermin D C-terminal domain Deposited 2017-08-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 277–484（208 aa） Fragment：unp residues 277-484
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；2.1 M DL-malic acid, pH 7.0
Resolution 2.90 Å R-free 0.290
6KMZ caspase-4 P22/P10 C258A in complex with human GSDMD-C domain Deposited 2019-08-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 287–480（194 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 200 mM sodium tartrate, 20% (w/v) polyethylene glycol 3350, 5% glycerol and 4% 1,1,1,3,3,3-hexafluoro-2-propanol
Resolution 3.61 Å R-free 0.319
6KMZ caspase-4 P22/P10 C258A in complex with human GSDMD-C domain Deposited 2019-08-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 286–480（195 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 200 mM sodium tartrate, 20% (w/v) polyethylene glycol 3350, 5% glycerol and 4% 1,1,1,3,3,3-hexafluoro-2-propanol
Resolution 3.61 Å R-free 0.319
6KN0 caspase-1 P20/P10 C285A in complex with human GSDMD-C domain Deposited 2019-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 283–480（198 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000
Resolution 2.79 Å R-free 0.300
6KN0 caspase-1 P20/P10 C285A in complex with human GSDMD-C domain Deposited 2019-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 283–480（198 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000
Resolution 2.79 Å R-free 0.300
6N9O Crystal structure of human GSDMD Deposited 2018-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–484（484 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT
Resolution 3.50 Å R-free 0.345
6N9O Crystal structure of human GSDMD Deposited 2018-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–484（484 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT
Resolution 3.50 Å R-free 0.345
6N9O Crystal structure of human GSDMD Deposited 2018-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–484（484 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT
Resolution 3.50 Å R-free 0.345
6N9O Crystal structure of human GSDMD Deposited 2018-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–484（484 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT
Resolution 3.50 Å R-free 0.345
7Z1X Crystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6 Deposited 2022-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–484（484 aa）
Chain D 1–484（484 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；293 K；20 mg/ml protein complex; 0.04 M NaCl, 25.8% (v/v) PEG400, 0.05 M Na3Cit pH 4.4
Resolution 1.86 Å R-free 0.249
9E0V GSDMD bound to a peptide Deposited 2024-10-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 276–484（209 aa） Fragment：MBP + GSD (UNP residues 276-484)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289.15 K；0.1 M HEPES, pH 7.5, 1.25 M sodium citrate dihydrate, 20 mM TCEP
Resolution 1.64 Å R-free 0.212

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GSDMD_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–241； UniProt 1–241 Author chain B； PDBConstruct 1–241； UniProt 1–241 Author chain C； PDBConstruct 1–241； UniProt 1–241 Author chain D； PDBConstruct 1–241； UniProt 1–241 Author chain E； PDBConstruct 1–241； UniProt 1–241 Author chain F； PDBConstruct 1–241； UniProt 1–241 Author chain G； PDBConstruct 1–241； UniProt 1–241 Author chain H； PDBConstruct 1–241； UniProt 1–241 Author chain I； PDBConstruct 1–241； UniProt 1–241 Author chain J； PDBConstruct 1–241； UniProt 1–241 Author chain K； PDBConstruct 1–241； UniProt 1–241 Author chain L； PDBConstruct 1–241； UniProt 1–241 Author chain M； PDBConstruct 1–241； UniProt 1–241 Author chain N； PDBConstruct 1–241； UniProt 1–241 Author chain O； PDBConstruct 1–241； UniProt 1–241 Author chain P； PDBConstruct 1–241； UniProt 1–241 Author chain Q； PDBConstruct 1–241； UniProt 1–241 Author chain R； PDBConstruct 1–241； UniProt 1–241 Author chain S； PDBConstruct 1–241； UniProt 1–241 Author chain T； PDBConstruct 1–241； UniProt 1–241 Author chain U； PDBConstruct 1–241； UniProt 1–241 Author chain V； PDBConstruct 1–241； UniProt 1–241 Author chain W； PDBConstruct 1–241； UniProt 1–241 Author chain X； PDBConstruct 1–241； UniProt 1–241 Author chain Y； PDBConstruct 1–241； UniProt 1–241 Author chain Z； PDBConstruct 1–241； UniProt 1–241 Author chain a； PDBConstruct 1–241； UniProt 1–241 Author chain b； PDBConstruct 1–241； UniProt 1–241 Author chain c； PDBConstruct 1–241； UniProt 1–241 Author chain d； PDBConstruct 1–241； UniProt 1–241 Author chain e； PDBConstruct 1–241； UniProt 1–241 Author chain f； PDBConstruct 1–241； UniProt 1–241 Author chain g； PDBConstruct 1–241； UniProt 1–241

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6vfe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vfe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6vfe
Deposition date deposition_date2020-01-03
Structure title titleGasdermin D pore
Keywords keywordsPore-forming protein, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron130.90 Å
Forward intensity I(0) i011018300000.00
Molecular weight molecular_weight878160.0 kDa
Excluded volume excluded_volume1091600 ų
Envelope volume envelope_volume3314000 ų
Hydration-shell volume shell_volume219650 ų
Envelope diameter envelope_diameter322.2 Å
Shell Rg shell_rg137.30 Å
Envelope Rg envelope_rg110.30 Å
Shape Rg shape_rg130.90 Å
Total Rg total_rg130.70 Å
Total atoms total_atoms61908
Residues n_residues7887
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax345.5 Å
Rg (real space) rg_real131.00 Å
Rg uncertainty (real space) rg_real_error1.46 Å
I(0) (real space) i0_real1.0950e+10
I(0) uncertainty (real space) i0_real_error2.3460e+08
Rg (reciprocal space) rg_reciprocal126.30 Å
I(0) (reciprocal space) i0_reciprocal10700000000.0000
Solution quality estimate total_estimate0.5861
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary230.3 Å
Skewness Skewness skewness-0.265
Kurtosis Kurtosis kurtosis-1.072
Angular range angular_range— – 0.0600 Å−1
Current regularization parameter α current_alpha0.6997
Highest regularization parameter α highest_alpha238300000.0000
Real-space data points n_real_points13
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.711; Stabil: 0.905; Sysdev: 0.000; Positv: 1.000; Valcen: 0.770; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)