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6x6c

Cryo-EM structure of NLRP1-DPP9-VbP complex

Method: ELECTRON MICROSCOPY Dmax: 142.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dipeptidyl peptidase 9

Homo sapiens

UniProt Q86TI2

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–863 Chain D； UniProt 1–863 Not recorded NACHT, LRR and PYD domains-containing protein 1 × 2 （Q9C000） GK2 [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；25 mM Tris pH 7.5, 150 mM NaCl, 1 mM TCEP cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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 6X6C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6EOQ DPP9 - Apo Deposited 2017-10-10 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 1–863（863 aa）
Chain C 1–863（863 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10%PEG 8000, 25% Glycerol, 0.16M Calcium Acetate, 0.08M Caodilate pH6.25,
Resolution 3.00 Å R-free 0.334
6EOQ DPP9 - Apo Deposited 2017-10-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–863（863 aa）
Chain D 1–863（863 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10%PEG 8000, 25% Glycerol, 0.16M Calcium Acetate, 0.08M Caodilate pH6.25,
Resolution 3.00 Å R-free 0.334
6EOR DPP9 - 1G244 Deposited 2017-10-10 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 1–863（863 aa）
Chain B 1–863（863 aa）
Not recorded 9XH (2~{S})-2-azanyl-4-[4-[bis(4-fluorophenyl)methyl]piperazin-1-yl]-1-(1,3-dihydroisoindol-2-yl)butane-1,4-dione × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG 8000, 25% Glycerol, 0.16M Calcium Acetate, 0.08M Cacodilate pH 6.25
Resolution 2.90 Å R-free 0.332
6EOR DPP9 - 1G244 Deposited 2017-10-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–863（863 aa）
Chain D 1–863（863 aa）
Not recorded 9XH (2~{S})-2-azanyl-4-[4-[bis(4-fluorophenyl)methyl]piperazin-1-yl]-1-(1,3-dihydroisoindol-2-yl)butane-1,4-dione × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG 8000, 25% Glycerol, 0.16M Calcium Acetate, 0.08M Cacodilate pH 6.25
Resolution 2.90 Å R-free 0.332
6QZV DPP9 bound to a dipeptide (MP) from the N-terminus of BRCA2 Deposited 2019-03-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–892（892 aa）
Chain B 1–892（892 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；20 mg/ml of protein, 10% PEG 8000, 25% glycerol, 0.16 M calcium acetate, 0.08 M cacodilate pH 6.25. Drops are set in a 1:1 ratio.
Resolution 3.00 Å R-free 0.345
6QZV DPP9 bound to a dipeptide (MP) from the N-terminus of BRCA2 Deposited 2019-03-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–892（892 aa）
Chain D 1–892（892 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；20 mg/ml of protein, 10% PEG 8000, 25% glycerol, 0.16 M calcium acetate, 0.08 M cacodilate pH 6.25. Drops are set in a 1:1 ratio.
Resolution 3.00 Å R-free 0.345
6X6A Cryo-EM structure of NLRP1-DPP9 complex Deposited 2020-05-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–863（863 aa）
Chain D 1–863（863 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris pH 7.5, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7A3F Crystal structure of apo DPP9 Deposited 2020-08-18 Different construct 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 1–892（892 aa）
Chain B 1–892（892 aa）
Not recorded PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.08 M Na-Cacodilate pH 5.25, 0.16 M Ca-Acetate, 30 % Glycerol, 10 % PEG 8K
Resolution 2.90 Å R-free 0.290
7A3F Crystal structure of apo DPP9 Deposited 2020-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–892（892 aa）
Chain D 1–892（892 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.08 M Na-Cacodilate pH 5.25, 0.16 M Ca-Acetate, 30 % Glycerol, 10 % PEG 8K
Resolution 2.90 Å R-free 0.290
7JKQ Human DPP9-CARD8 complex Deposited 2020-07-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–863（863 aa）
Chain D 1–863（863 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM HEPES, pH 7.5, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JN7 Human DPP9-CARD8 complex Deposited 2020-08-04 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–863（863 aa）
Chain D 1–863（863 aa）
Not recorded GK2 [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7SVL DPP9 IN COMPLEX WITH LIGAND ICeD-2 Deposited 2021-11-19 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 1–863（863 aa）
Chain B 1–863（863 aa）
Not recorded D06 (2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；10% PEG 8000 25% Glycerol 0.16 M Calcium Acetate 0.08 M Cacodilate pH 6.25
Resolution 2.46 Å R-free 0.341
7SVL DPP9 IN COMPLEX WITH LIGAND ICeD-2 Deposited 2021-11-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–863（863 aa）
Chain D 1–863（863 aa）
Not recorded D06 (2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；10% PEG 8000 25% Glycerol 0.16 M Calcium Acetate 0.08 M Cacodilate pH 6.25
Resolution 2.46 Å R-free 0.341
7SVN DPP9 IN COMPLEX WITH LIGAND ICeD-1 Deposited 2021-11-19 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 1–863（863 aa）
Chain B 1–863（863 aa）
Not recorded CW8 (2S,4S)-1-[(2S)-2-amino-2-cyclohexylacetyl]-4-fluoropyrrolidine-2-carbonitrile × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；10% PEG 8000 25% glycerol 0.16 M calcium acetate 0.08 M cacodilate pH 6.25
Resolution 2.78 Å R-free 0.349
7SVN DPP9 IN COMPLEX WITH LIGAND ICeD-1 Deposited 2021-11-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–863（863 aa）
Chain D 1–863（863 aa）
Not recorded CW8 (2S,4S)-1-[(2S)-2-amino-2-cyclohexylacetyl]-4-fluoropyrrolidine-2-carbonitrile × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；10% PEG 8000 25% glycerol 0.16 M calcium acetate 0.08 M cacodilate pH 6.25
Resolution 2.78 Å R-free 0.349
7ZXS Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295 Deposited 2022-05-22 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 20–863（844 aa） Fragment：extcolor{red}{>FRAGMENT<}
Chain C 20–863（844 aa） Fragment：extcolor{red}{>FRAGMENT<}
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) KBO 2-ethyl-2-methanoyl-~{N}-[3-[[4-(quinolin-8-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide × 2 EDO 1,2-ETHANEDIOL × 17 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The crystal is grown in a condition containing PEG 2K MME buffered by Tris pH 7
Resolution 1.81 Å R-free 0.203
7ZXS Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295 Deposited 2022-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 20–863（844 aa）
Chain D 20–863（844 aa）
Not recorded KBO 2-ethyl-2-methanoyl-~{N}-[3-[[4-(quinolin-8-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide × 2 EDO 1,2-ETHANEDIOL × 24 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The crystal is grown in a condition containing PEG 2K MME buffered by Tris pH 7
Resolution 1.81 Å R-free 0.203
9GOC Crystal structure of DPP9 Ser730Ala in complex with sulphostin. Deposited 2024-09-05 Different construct 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 20–863（844 aa）
Chain B 20–863（844 aa）
Not recorded A1INE Sulphostin × 2 EDO 1,2-ETHANEDIOL × 28 PEG DI(HYDROXYETHYL)ETHER × 2 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG2000 MME 20% (w/v), 0.1 M Tris pH 6.75
Resolution 1.89 Å R-free 0.199
9GOC Crystal structure of DPP9 Ser730Ala in complex with sulphostin. Deposited 2024-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 20–863（844 aa）
Chain D 20–863（844 aa）
Not recorded A1INE Sulphostin × 2 EDO 1,2-ETHANEDIOL × 19 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG2000 MME 20% (w/v), 0.1 M Tris pH 6.75
Resolution 1.89 Å R-free 0.199
9GOD Crystal structure of DPP9 in complex with N-phosphono-(S)-3-aminopiperidine-2-one-based inhibitor Deposited 2024-09-05 Different construct 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 20–863（844 aa）
Chain D 20–863（844 aa）
Not recorded A1INH ethoxy-[2-(4-pentylphenyl)sulfanylethyl]phosphinous acid × 2 EDO 1,2-ETHANEDIOL × 12 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18.0% w/v PEG 2K MME; 0.1 M Tris pH 7.25
Resolution 2.49 Å R-free 0.219
9GOD Crystal structure of DPP9 in complex with N-phosphono-(S)-3-aminopiperidine-2-one-based inhibitor Deposited 2024-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 20–863（844 aa）
Chain C 20–863（844 aa）
Not recorded A1INH ethoxy-[2-(4-pentylphenyl)sulfanylethyl]phosphinous acid × 2 EDO 1,2-ETHANEDIOL × 23 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18.0% w/v PEG 2K MME; 0.1 M Tris pH 7.25
Resolution 2.49 Å R-free 0.219
9GON Crystal structure of DPP9 in complex with sulphostin Deposited 2024-09-05 Different construct 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 20–863（844 aa）
Chain B 20–863（844 aa）
Not recorded A1INF azanyl-oxidanylidene-(sulfoamino)phosphanium × 2 PEG DI(HYDROXYETHYL)ETHER × 3 EDO 1,2-ETHANEDIOL × 37 CL CHLORIDE ION × 7 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) PEG 2000 MME, 0.1M Tris pH 6.75
Resolution 1.89 Å R-free 0.206
9GON Crystal structure of DPP9 in complex with sulphostin Deposited 2024-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 20–863（844 aa）
Chain D 20–863（844 aa）
Not recorded A1INF azanyl-oxidanylidene-(sulfoamino)phosphanium × 2 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 34 CL CHLORIDE ION × 5 NA SODIUM ION × 3 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) PEG 2000 MME, 0.1M Tris pH 6.75
Resolution 1.89 Å R-free 0.206

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

View Construct and Data Evidence
UniProt name DPP9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 29–891； UniProt 1–863 Author chain D； PDBConstruct 29–891； UniProt 1–863

NACHT, LRR and PYD domains-containing protein 1

Homo sapiens

UniProt Q9C000

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 1–1473 Chain F； UniProt 1–1473 Not recorded Dipeptidyl peptidase 9 × 2 （Q86TI2） GK2 [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；25 mM Tris pH 7.5, 150 mM NaCl, 1 mM TCEP cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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 6X6C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1PN5 NMR structure of the NALP1 Pyrin domain (PYD) Deposited 2003-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–93（93 aa） Fragment：Pyrin domain (PYD)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Pressure 1
NMR sample composition 1mM NALP1 PYD U-15N,13C; 50mM Na / PO4 - Buffer; 50mM NaCl; 1mM CHAPS; 20mM DTT (D10); 0.02% NaN3; 0.1mM EDTA; protease inhibitor cocktail (Complete, Roche); 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
3KAT Crystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E Deposited 2009-10-19 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 1371–1467（97 aa） Fragment：CARD domain
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.260
3KAT Crystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E Deposited 2009-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1371–1467（97 aa） Fragment：CARD domain
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.260
4IFP X-ray Crystal Structure of Human NLRP1 CARD Domain Deposited 2012-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1335–1418（84 aa） Fragment：NLRP1-CARD
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.208
4IFP X-ray Crystal Structure of Human NLRP1 CARD Domain Deposited 2012-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1335–1418（84 aa） Fragment：NLRP1-CARD
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.208
4IFP X-ray Crystal Structure of Human NLRP1 CARD Domain Deposited 2012-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1335–1418（84 aa） Fragment：NLRP1-CARD
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.208
4IM6 LRR domain from human NLRP1 Deposited 2013-01-02 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 791–990（200 aa） Fragment：LRR domain (UNP Residues 791-990)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris pH 8.0, 0.02 M MgCl2, 25 % (w/v) PAA 5100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.183
4IM6 LRR domain from human NLRP1 Deposited 2013-01-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 791–990（200 aa） Fragment：LRR domain (UNP Residues 791-990)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris pH 8.0, 0.02 M MgCl2, 25 % (w/v) PAA 5100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.183
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 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 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
6K7V Structure of NLRP1 CARD filament Deposited 2019-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 1379–1466（88 aa）
Chain B 1379–1466（88 aa）
Chain C 1379–1466（88 aa）
Chain D 1379–1466（88 aa）
Chain E 1379–1466（88 aa）
Chain F 1379–1466（88 aa）
Chain G 1379–1466（88 aa）
Chain H 1379–1466（88 aa）
Chain I 1379–1466（88 aa）
Chain J 1379–1466（88 aa）
Chain K 1379–1466（88 aa）
Chain L 1379–1466（88 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å R-free 0.285
6X6A Cryo-EM structure of NLRP1-DPP9 complex Deposited 2020-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1212（1212 aa）
Chain C 1213–1473（261 aa）
Chain E 1–1212（1212 aa）
Chain F 1213–1473（261 aa）
Chain G 1213–1473（261 aa）
Chain I 1213–1473（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris pH 7.5, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6XKK Cryo-EM structure of the NLRP1-CARD filament Deposited 2020-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 44 PDB declaration: 44-meric
Chain A 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain B 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain C 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain D 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain E 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain F 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain G 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain H 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain I 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain J 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain K 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain L 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain M 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain N 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain O 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain P 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain Q 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain R 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain S 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain T 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain U 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain V 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain a 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain b 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain c 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain d 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain e 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain f 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain g 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain h 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain i 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain j 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain k 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain l 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain m 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain n 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain o 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain p 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain q 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain r 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain s 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain t 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain u 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain v 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
7WGE Human NLRP1 complexed with thioredoxin Deposited 2021-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 95–994（900 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8ZGD The Crystal Structure of the NLRP1_LRR domain from Biortus. Deposited 2024-05-09 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 791–990（200 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20mM MgCl2, 0.1M Tris pH 8.0, 19% polyacrylic acid 5100
Resolution 2.05 Å R-free 0.221
9BJ9 Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron Deposited 2024-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 131–139（9 aa） Fragment：residues 131-139 (Uniprot numbering)
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å

11 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NLRP1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–1473； UniProt 1–1473 Author chain F； PDBConstruct 1–1473； UniProt 1–1473

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 6x6c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6x6c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6x6c
Deposition date deposition_date2020-05-27
Structure title titleCryo-EM structure of NLRP1-DPP9-VbP complex
Keywords keywordsNLRP1, DPP9, inflammasome, Val-boroPro (VbP), talabostat, innate immunity, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.00 Å
Radius of gyration Rg (electron density) rg_electron42.77 Å
Forward intensity I(0) i0711458000.00
Molecular weight molecular_weight224070.0 kDa
Excluded volume excluded_volume281570 ų
Envelope volume envelope_volume366380 ų
Hydration-shell volume shell_volume70416 ų
Envelope diameter envelope_diameter153.8 Å
Shell Rg shell_rg48.60 Å
Envelope Rg envelope_rg42.50 Å
Shape Rg shape_rg42.75 Å
Total Rg total_rg43.10 Å
Total atoms total_atoms15834
Residues n_residues1963
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 dmax142.1 Å
Rg (real space) rg_real42.99 Å
Rg uncertainty (real space) rg_real_error1.52 Å
I(0) (real space) i0_real7.1150e+08
I(0) uncertainty (real space) i0_real_error1.3640e+07
Rg (reciprocal space) rg_reciprocal43.01 Å
I(0) (reciprocal space) i0_reciprocal711500000.0000
Solution quality estimate total_estimate0.8876
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.1 Å
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.473
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha150300000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.880
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6x6cA01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
Domain ID domain_id6x6cD01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
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8. Citations (1)

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9. Files and Curves (10)