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9l4k

Structure of human NLRP2-TLE6-OOEP complex

Method: ELECTRON MICROSCOPY Dmax: 188.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 2

Homo sapiens

UniProt Q9NX02

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1062 Not recorded Transducin-like enhancer protein 6 × 1 （Q9H808） Oocyte-expressed protein homolog × 1 （A6NGQ2） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.41 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 9L4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9C6V Crystal Structure of a single chain trimer composed of HLA-B*39:06 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2 (1 molecule/asymmetric unit) Deposited 2024-06-09 Different construct 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 323–331（9 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M Potassium sulfate
Resolution 1.70 Å R-free 0.219
9C6W Crystal Structure of a single chain trimer composed of HLA-B*39:06 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2 (2 molecules/asymmetric unit) Deposited 2024-06-09 Different construct 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 323–331（9 aa）
Not recorded SO4 SULFATE ION × 7 EDO 1,2-ETHANEDIOL × 8 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；2M Ammonuim sulfate,0.2 M Lithium sulfate, 0.1 M HEPES
Resolution 1.70 Å R-free 0.215
9C6W Crystal Structure of a single chain trimer composed of HLA-B*39:06 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2 (2 molecules/asymmetric unit) Deposited 2024-06-09 Different construct 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 323–331（9 aa）
Not recorded SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 2 P3G 3,6,9,12,15-PENTAOXAHEPTADECANE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；2M Ammonuim sulfate,0.2 M Lithium sulfate, 0.1 M HEPES
Resolution 1.70 Å R-free 0.215
9C6X Crystal Structure of a single chain trimer composed of HLA-B*39:01 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2 Deposited 2024-06-09 Different construct 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 323–331（9 aa）
Not recorded P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；25% PEG 3350 and 0.1 M Tris
Resolution 1.70 Å R-free 0.232
9L4L Structure of human SCMCcore complex contain NLRP2 Deposited 2024-12-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1062（1062 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out in argon atmosphere
Resolution 3.40 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NALP2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1062； UniProt 1–1062

Transducin-like enhancer protein 6

Homo sapiens

UniProt Q9H808

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–572 Not recorded NACHT, LRR and PYD domains-containing protein 2 × 1 （Q9NX02） Oocyte-expressed protein homolog × 1 （A6NGQ2） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.41 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 9L4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8X7V Structure of human SCMC ternary complex Deposited 2023-11-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 146–572（427 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8X7W Structure of dimeric human SCMC complex Deposited 2023-11-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 146–572（427 aa）
Chain F 146–572（427 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9L4L Structure of human SCMCcore complex contain NLRP2 Deposited 2024-12-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–572（572 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out in argon atmosphere
Resolution 3.40 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TLE6_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–572； UniProt 1–572

Oocyte-expressed protein homolog

Homo sapiens

UniProt A6NGQ2

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–149 Not recorded NACHT, LRR and PYD domains-containing protein 2 × 1 （Q9NX02） Transducin-like enhancer protein 6 × 1 （Q9H808） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.41 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 9L4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8X7V Structure of human SCMC ternary complex Deposited 2023-11-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–149（149 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8X7W Structure of dimeric human SCMC complex Deposited 2023-11-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–149（149 aa）
Chain E 1–149（149 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9L4L Structure of human SCMCcore complex contain NLRP2 Deposited 2024-12-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–149（149 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25mM Tris pH 8.0, 150mM NaCl,5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out in argon atmosphere
Resolution 3.40 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OOEP_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–149； UniProt 1–149

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 9l4k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9l4k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9l4k
Deposition date deposition_date2024-12-20
Structure title titleStructure of human NLRP2-TLE6-OOEP complex
Keywords keywordscomplex, CYTOSOLIC PROTEIN; CYTOSOLIC 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_guinier51.49 Å
Radius of gyration Rg (electron density) rg_electron52.49 Å
Forward intensity I(0) i0284845000.00
Molecular weight molecular_weight140140.0 kDa
Excluded volume excluded_volume175810 ų
Envelope volume envelope_volume272090 ų
Hydration-shell volume shell_volume47318 ų
Envelope diameter envelope_diameter198.5 Å
Shell Rg shell_rg48.69 Å
Envelope Rg envelope_rg52.32 Å
Shape Rg shape_rg52.57 Å
Total Rg total_rg52.04 Å
Total atoms total_atoms9832
Residues n_residues1256
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 dmax188.2 Å
Rg (real space) rg_real52.12 Å
Rg uncertainty (real space) rg_real_error3.01 Å
I(0) (real space) i0_real2.8480e+08
I(0) uncertainty (real space) i0_real_error6.1110e+06
Rg (reciprocal space) rg_reciprocal50.95 Å
I(0) (reciprocal space) i0_reciprocal284400000.0000
Solution quality estimate total_estimate0.7076
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4 Å
Skewness Skewness skewness0.605
Kurtosis Kurtosis kurtosis-0.290
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18620000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.490; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.257; Smooth: 0.468
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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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8. Citations (1)

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9. Files and Curves (10)