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7jkq

Human DPP9-CARD8 complex

Method: ELECTRON MICROSCOPY Dmax: 142.7 Å Quality: REASONABLE
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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 Caspase recruitment domain-containing protein 8 × 2 （Q9Y2G2） 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

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 7JKQ 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 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 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 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 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 experimental conditions 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
6X6C Cryo-EM structure of NLRP1-DPP9-VbP complex Deposited 2020-05-27 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 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
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
7JN7 Human DPP9-CARD8 complex Deposited 2020-08-04 Different ligand/ion Different experimental conditions 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 1–863； UniProt 1–863 Author chain D； PDBConstruct 1–863； UniProt 1–863

Caspase recruitment domain-containing protein 8

Homo sapiens

UniProt Q9Y2G2

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 B； UniProt 1–537 Chain C； UniProt 1–537 Not recorded Dipeptidyl peptidase 9 × 2 （Q86TI2） 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

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 7JKQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4IKM X-ray structure of CARD8 CARD domain Deposited 2012-12-26 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 345–431（87 aa） Fragment：MBP tagged human CARD8 CARD domain
Non-standard monomer：Yes (specific site not provided by mmCIF) IOD IODIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；16% PEG8000, 0.1 M NaI, 0.1 M NaAc, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.46 Å R-free 0.253
6K9F Structure of unknow protein 4 Deposited 2019-06-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 345–431（87 aa）
Chain B 345–431（87 aa）
Chain C 345–431（87 aa）
Chain D 345–431（87 aa）
Chain E 345–431（87 aa）
Chain F 345–431（87 aa）
Chain G 345–431（87 aa）
Chain H 345–431（87 aa）
Chain I 345–431（87 aa）
Chain J 345–431（87 aa）
Chain K 345–431（87 aa）
Chain L 345–431（87 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 0.302
6XKJ Cryo-EM structure of CARD8-CARD filament Deposited 2020-06-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric
Chain A 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain B 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain C 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain D 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain E 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain F 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain G 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain H 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain I 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain J 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain K 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain L 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain M 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain N 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain O 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Chain P 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7JN7 Human DPP9-CARD8 complex Deposited 2020-08-04 Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–537（537 aa）
Chain C 1–537（537 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CARD8_HUMAN
Isoform Q9Y2G2-5
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–537； UniProt 1–537 Author chain C； PDBConstruct 1–537； UniProt 1–537

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 7jkq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7jkq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7jkq
Deposition date deposition_date2020-07-28
Structure title titleHuman DPP9-CARD8 complex
Keywords keywordsCARD8, DPP9, inflammasome, Val-boroPro (VbP), talabostat, innate immunity, IMMUNE SYSTEM, HYDROLASE; IMMUNE SYSTEM, HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.60 Å
Radius of gyration Rg (electron density) rg_electron43.26 Å
Forward intensity I(0) i0765320000.00
Molecular weight molecular_weight232370.0 kDa
Excluded volume excluded_volume291920 ų
Envelope volume envelope_volume390960 ų
Hydration-shell volume shell_volume73902 ų
Envelope diameter envelope_diameter153.2 Å
Shell Rg shell_rg49.33 Å
Envelope Rg envelope_rg42.76 Å
Shape Rg shape_rg43.25 Å
Total Rg total_rg43.57 Å
Total atoms total_atoms16437
Residues n_residues2048
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 dmax142.7 Å
Rg (real space) rg_real43.53 Å
Rg uncertainty (real space) rg_real_error1.00 Å
I(0) (real space) i0_real7.6530e+08
I(0) uncertainty (real space) i0_real_error1.3490e+07
Rg (reciprocal space) rg_reciprocal43.60 Å
I(0) (reciprocal space) i0_reciprocal765400000.0000
Solution quality estimate total_estimate0.6622
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.6 Å
Skewness Skewness skewness0.262
Kurtosis Kurtosis kurtosis-0.476
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha123800000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 0.005; Positv: 1.000; Valcen: 1.000; Smooth: 0.873
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7jkqA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id7jkqA02
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_id7jkqD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id7jkqD02
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)