SAXSdb — 8swf

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 3

Homo sapiens

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 130–1036 Chain B； UniProt 130–1036 Chain C； UniProt 130–1036 Chain D； UniProt 130–1036 Chain E； UniProt 130–1036 Chain F； UniProt 130–1036 Chain G； UniProt 130–1036 Chain H； UniProt 130–1036	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.39 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 8SWF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NAQ 3D NMR solution structure of NLRP3 PYD Deposited 2016-01-07	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 3–93（91 aa） Fragment：Pyrin domain residues 3-93	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.6；303 K；Ionic strength (raw mmCIF value) 0.0051；Pressure ambient NMR sample composition 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3QF2 Crystal structure of NALP3 PYD Deposited 2011-01-21	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 3–112（110 aa） Fragment：PYD domain, DAPIN domain, residues 3-112	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M ammonium citrate, 0.1M sodium acetate pH4.6, 30% PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.235
3QF2 Crystal structure of NALP3 PYD Deposited 2011-01-21	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 3–112（110 aa） Fragment：PYD domain, DAPIN domain, residues 3-112	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M ammonium citrate, 0.1M sodium acetate pH4.6, 30% PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.235
6NPY Cryo-EM structure of NLRP3 bound to NEK7 Deposited 2019-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–1036（1034 aa）	Mutation：D133I, R135C, K136A, K140A	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7ALV Crystal Structure of NLRP3 NACHT domain in complex with a potent inhibitor Deposited 2020-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa） Fragment：NACHT domain	Not recorded	RM5 1-[4-chloranyl-2,6-di(propan-2-yl)phenyl]-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M Hepes pH 7.5, 1.4M SodiumCitrate	Resolution 2.83 Å R-free 0.265
7PZC Cryo-EM structure of the NLRP3 decamer bound to the inhibitor CRID3 Deposited 2021-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–1036（1036 aa） Chain B 1–1036（1036 aa） Chain C 1–1036（1036 aa） Chain D 1–1036（1036 aa） Chain E 1–1036（1036 aa） Chain F 1–1036（1036 aa） Chain G 1–1036（1036 aa） Chain H 1–1036（1036 aa） Chain I 1–1036（1036 aa） Chain J 1–1036（1036 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 10 8GI 1-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 10 mM MgCl2, 1 mM ADP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7PZD Cryo-EM structure of the NLRP3 PYD filament Deposited 2021-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain G 3–110（108 aa） Chain H 3–110（108 aa） Chain I 3–110（108 aa） Chain J 3–110（108 aa） Chain K 3–110（108 aa） Chain L 3–110（108 aa） Chain M 3–110（108 aa） Chain N 3–110（108 aa） Chain O 3–110（108 aa） Chain P 3–110（108 aa） Chain Q 3–110（108 aa） Chain R 3–110（108 aa） Chain S 3–110（108 aa） Chain T 3–110（108 aa） Chain U 3–110（108 aa） Chain V 3–110（108 aa） Chain W 3–110（108 aa） Chain X 3–110（108 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7VTP Cryo-EM structure of PYD-deleted human NLRP3 hexamer Deposited 2021-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 130–1036（907 aa） Chain B 130–1036（907 aa） Chain C 130–1036（907 aa） Chain D 130–1036（907 aa） Chain E 130–1036（907 aa） Chain F 130–1036（907 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 7YN 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH (pH 7.5), 0.2 M NaCl, 1 mM MgCl2, 0.5 mM TCEP, 1.0 mM ADP, 0.05 mM MCC950 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
7ZGU Human NLRP3-deltaPYD hexamer Deposited 2022-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 126–1036（911 aa） Chain B 126–1036（911 aa） Chain C 126–1036（911 aa） Chain D 126–1036（911 aa） Chain E 126–1036（911 aa） Chain F 126–1036（911 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8EJ4 Cryo-EM structure of the active NLRP3 inflammasome disk Deposited 2022-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 133–1034（902 aa） Chain B 133–1034（902 aa） Chain C 133–1034（902 aa） Chain D 133–1034（902 aa） Chain E 133–1034（902 aa） Chain F 133–1034（902 aa） Chain G 133–1034（902 aa） Chain H 133–1034（902 aa） Chain I 133–1034（902 aa） Chain J 133–1034（902 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 10 MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8ERT NLRP3 PYD filament Deposited 2022-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 21 PDB declaration: 21-meric	Chain A 1–95（95 aa） Chain B 1–95（95 aa） Chain C 1–95（95 aa） Chain D 1–95（95 aa） Chain E 1–95（95 aa） Chain F 1–95（95 aa） Chain G 1–95（95 aa） Chain I 1–95（95 aa） Chain J 1–95（95 aa） Chain K 1–95（95 aa） Chain L 1–95（95 aa） Chain M 1–95（95 aa） Chain N 1–95（95 aa） Chain O 1–95（95 aa） Chain Q 1–95（95 aa） Chain R 1–95（95 aa） Chain S 1–95（95 aa） Chain U 1–95（95 aa） Chain V 1–95（95 aa） Chain W 1–95（95 aa） Chain X 1–95（95 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8ETR CryoEM Structure of NLRP3 NACHT domain in complex with G2394 Deposited 2022-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–676（543 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WTN (6S,8R)-N-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5H-pyrazolo[5,1-b][1,3]oxazine-3-sulfonamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；0.15M NaCl, 20mM Tris pH 7.5, 10% glycerol, 1mM TCEP, 2.5mM ATP, 2mM MgCl2. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8RI2 Crystal structure of NLRP3 in complex with inhibitor NP3-562 Deposited 2023-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1H02 2-[4-chloranyl-9-oxidanylidene-12-(2-oxidanylpropan-2-yl)-5-thia-1,10,11-triazatricyclo[6.4.0.0^{2,6}]dodeca-2(6),3,7,11-tetraen-10-yl]-~{N}-[(3~{R})-1-methylpiperidin-3-yl]ethanamide × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；protein: well = 1: 1 well: 1.94 M Ammonium citrate pH 7.0 protein: 7 mg/ml protein copurified with 1 uM inhibitor	Resolution 2.80 Å R-free 0.270
8SWK Cryo-EM structure of NLRP3 closed hexamer Deposited 2023-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–1036（904 aa） Chain B 133–1036（904 aa） Chain C 133–1036（904 aa） Chain D 133–1036（904 aa） Chain E 133–1036（904 aa） Chain F 133–1036（904 aa）	Not recorded	7YN 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.32 Å
8SXN Structure of NLRP3 and NEK7 complex Deposited 2023-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 133–1036（904 aa） Chain D 133–1036（904 aa）	Not recorded	7YN 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.04 Å
8WSM NLRP3 NACHT domain in complex with compound 32 Deposited 2023-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 XE3 2-[[2-methyl-5-(trifluoromethyl)phenyl]amino]-~{N}-(1,4-oxazepan-4-ylsulfonyl)-1,3-oxazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Tris pH 7.5, 1.2 M sodium citrate	Resolution 2.70 Å R-free 0.248
8ZEM Crystal Structure of NLRP3 NACHT domain in complex with NP3-1 Deposited 2024-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1D79 1-[5-[2,3-bis(chloranyl)phenyl]-2,3-dihydro-1~{H}-inden-4-yl]-3-[4-(2-oxidanylpropan-2-yl)thiophen-2-yl]sulfonyl-urea × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；23~25 % w/v Polyethylene glycol monomethyl ether 5,000 ;100 mM MES pH 6.3~6.7 ;200 mM Ammonium sulfate	Resolution 3.32 Å R-free 0.347
9DH3 Cryo-EM structure of NLRP3 complex with Compound C Deposited 2024-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 136–1036（901 aa） Chain B 136–1036（901 aa） Chain C 136–1036（901 aa） Chain D 136–1036（901 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 A1A4L 2-[(4S)-5-ethyl-8-oxothieno[2',3':4,5]pyrrolo[1,2-d][1,2,4]triazin-7(8H)-yl]-N-(pyrimidin-4-yl)acetamide × 4 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.76 Å
9GU4 Crystal structure of NLRP3 in complex with inhibitor NP3-253 Deposited 2024-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1IPJ 2-[6-[[(3R)-1-ethylpiperidin-3-yl]amino]pyridazin-3-yl]-3-methyl-5-(trifluoromethyl)phenol × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；protein: well = 1: 1 well: 1.94 M Ammonium citrate pH 7.0 protein: 7 mg/ml, 1mM inhibitor co-complex	Resolution 2.70 Å R-free 0.264
9HG4 NACHT domain of NLRP3 in complex with DFV890 Deposited 2024-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1IUG 1-[azanyl-oxidanylidene-[2-(2-oxidanylpropan-2-yl)-1,3-thiazol-5-yl]-$l^{6}-sulfanylidene]-3-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)urea × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；protein: 0.2 ul NLRP3 (131-679) at 7 mg/ml in 50mM HEPES pH 7.8, 500mM NaCl, 10% glycerol, 1mM MgCl2, 1mM TCEP, 100uM ADP, and 0.8 mM DFV890 (in DMSO) wel: 0.2 ul 1.99M NH4 3 citrate	Resolution 2.77 Å R-free 0.264
9MGY Cryo-EM structure of Human NLRP3 complex with compound 1 Deposited 2024-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–1036（1036 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 A1BLR (2M)-2-(6-{[(3R)-1-methylpiperidin-3-yl]amino}pyridazin-3-yl)-5-(trifluoromethyl)phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9MIE Human NLRP3 complex with compound 2 in the closed hexamer Deposited 2024-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–1036（1036 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 A1BLP (2P)-2-(4-{[(3R)-1-methylpiperidin-3-yl]amino}-6,7-dihydro-5H-cyclopenta[d]pyridazin-1-yl)-5-(trifluoromethyl)phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9MIG Cryo-EM structure of Human NLRP3 complex with compound 3 Deposited 2024-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–1036（1036 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 A1BLQ (2P)-2-(4-{[(3R)-1-methylpiperidin-3-yl]amino}-5,6,7,8-tetrahydrophthalazin-1-yl)-5-(trifluoromethyl)phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9SFG Crystal structure of NLRP3 in complex with inhibitor NP3-742 Deposited 2025-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1JNK 5-methyl-~{N}-[(3~{R})-1-methylpiperidin-3-yl]-6-(2-methyl-1~{H}-pyrrolo[2,3-b]pyridin-6-yl)pyridazin-3-amine × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；protein: well = 1: 1 well: 1.94 M Ammonium citrate pH 7.0 protein: 7 mg/ml, 1mM inhibitor co-complex	Resolution 3.20 Å R-free 0.279

23 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLRP3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–910； UniProt 130–1036 Author chain B； PDBConstruct 4–910； UniProt 130–1036 Author chain C； PDBConstruct 4–910； UniProt 130–1036 Author chain D； PDBConstruct 4–910； UniProt 130–1036 Author chain E； PDBConstruct 4–910； UniProt 130–1036 Author chain F； PDBConstruct 4–910； UniProt 130–1036 Author chain G； PDBConstruct 4–910； UniProt 130–1036 Author chain H； PDBConstruct 4–910； UniProt 130–1036

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8swf
Deposition date deposition_date	2023-05-18
最后修订 last_revision	2024-02-14
Structure title title	Cryo-EM structure of NLRP3 open octamer
Keywords keywords	Activated NLRP3, Cryo-EM, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	71.89 Å
Radius of gyration Rg (electron density) rg_electron	71.36 Å
Forward intensity I(0) i0	7800710000.00
Molecular weight molecular_weight	760180.0 kDa
Excluded volume excluded_volume	956720 Å³
Envelope volume envelope_volume	1712600 Å³
Hydration-shell volume shell_volume	202180 Å³
Envelope diameter envelope_diameter	219.6 Å
Shell Rg shell_rg	76.85 Å
Envelope Rg envelope_rg	65.30 Å
Shape Rg shape_rg	71.38 Å
Total Rg total_rg	71.39 Å
Total atoms total_atoms	53244
Residues n_residues	6676
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	228.0 Å
Rg (real space) rg_real	71.49 Å
Rg uncertainty (real space) rg_real_error	2.51 Å
I(0) (real space) i0_real	7.8010e+09
I(0) uncertainty (real space) i0_real_error	1.7380e+08
Rg (reciprocal space) rg_reciprocal	73.16 Å
I(0) (reciprocal space) i0_reciprocal	7826000000.0000
Solution quality estimate total_estimate	0.8611
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	103.6 Å
Skewness Skewness skewness	-0.081
Kurtosis Kurtosis kurtosis	-0.567
Angular range angular_range	— – 0.1100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	368500000.0000
Real-space data points n_real_points	23
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.795

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Description description	NACHT, LRR and PYD domains-containing protein 3
Molecular weight formula_weight	103675.7 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	53244

AEYCKMKKDYRKKYRKYVRSRFQCIEDRNARLGESVSLNKRYTRLRLIKEHRSQQEREQELLAIGKTKTCESPVSPIKMELLFDPDDEHSEPVHTVVFQGAAGIGKTILARKMMLDWASGTLYQDRFDYLFYIHCREVSLVTQRSLGDLIMSCCPDPNPPIHKIVRKPSRILFLMDGFDELQGAFDEHIGPLCTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQHLLDHPRHVEILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCTGLKQQMESGKSLAQTSKTTTAVYVFFLSSLLQPRGGSQEHGLCAHLWGLCSLAADGIWNQKILFEESDLRNHGLQKADVSAFLRMNLFQKEVDCEKFYSFIHMTFQEFFAAMYYLLEEEKEGRTNVPGSRLKLPSRDVTVLLENYGKFEKGYLIFVVRFLFGLVNQERTSYLEKKLSCKISQQIRLELLKWIEVKAKAKKLQIQPSQLELFYCLYEMQEEDFVQRAMDYFPKIEINLSTRMDHMVSSFCIENCHRVESLSLGFLHNMPKEEEEEEKEGRHLDMVQCVLPSSSHAACSHGLVNSHLTSSFCRGLFSVLSTSQSLTELDLSDNSLGDPGMRVLCETLQHPGCNIRRLWLGRCGLSHECCFDISLVLSSNQKLVELDLSDNALGDFGIRLLCVGLKHLLCNLKKLWLVSCCLTSACCQDLASVLSTSHSLTRLYVGENALGDSGVAILCEKAKNPQCNLQKLGLVNSGLTSVCCSALSSVLSTNQNLTHLYLRGNTLGDKGIKLLCEGLLHPDCKLQVLELDNCNLTSHCCWDLSTLLTSSQSLRKLSLGNNDLGDLGVMMFCEVLKQQSCLLQNLGLSEMYFNYETKSALETLQEEKPELTVVFEPSW

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.39 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	466664

fit	/app/data/saxs_computation/sw/8swf/8swf.fit
pddf	/app/data/pr_computation/sw/8swf/8swf.pr.out
profile	/app/data/saxs_computation/sw/8swf/8swf.dat

Cryo-EM structure of NLRP3 open octamer

1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)