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9wsr

Structure of mouse NLRP14-KDM2A-SKP1 complex

Method: ELECTRON MICROSCOPY Dmax: 118.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific demethylase 2A

Mus musculus

UniProt P59997

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 815–1161 Not recorded S-phase kinase-associated protein 1 × 1 （Q9WTX5） NACHT, LRR and PYD domains-containing protein 14 × 1 （Q6B966） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.79 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 9WSR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4TN7 Crystal structure of mouse KDM2A-H3K36ME-NO complex Deposited 2014-06-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–364（329 aa） Fragment：UNP residues 36-364
Chain B 450–517（68 aa） Fragment：UNP residues 450-517
Not recorded FE FE (III) ION × 1 NO NITRIC OXIDE × 1 SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM Li-citrate 18-30% PEG 3350
Resolution 2.20 Å R-free 0.279
4TN7 Crystal structure of mouse KDM2A-H3K36ME-NO complex Deposited 2014-06-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 36–364（329 aa） Fragment：UNP residues 36-364
Chain D 450–517（68 aa） Fragment：UNP residues 450-517
Not recorded FE FE (III) ION × 1 SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM Li-citrate 18-30% PEG 3350
Resolution 2.20 Å R-free 0.279
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 36–364（329 aa） Fragment：UNP residues 36-364
Chain B 450–517（68 aa） Fragment：UNP residues 450-517
Not recorded FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350
Resolution 1.98 Å R-free 0.237
7UVA Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015 Deposited 2022-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 36–364（329 aa） Fragment：UNP residues 36-364
Chain E 450–517（68 aa） Fragment：UNP residues 450-517
Not recorded FE FE (III) ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris-Cl, pH 8.5, 150 mM lithium sulfate, 20% PEG3350
Resolution 1.98 Å R-free 0.237
9WSQ Structure of dimeric mouse NLRP14-KDM2A-SKP1 complex Deposited 2025-09-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 815–1161（347 aa）
Chain E 815–1161（347 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å

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

View Construct and Data Evidence
UniProt name KDM2A_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 12–358； UniProt 815–1161

S-phase kinase-associated protein 1

Mus musculus

UniProt Q9WTX5

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 1–163 Not recorded Lysine-specific demethylase 2A × 1 （P59997） NACHT, LRR and PYD domains-containing protein 14 × 1 （Q6B966） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.79 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 9WSR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
12DL Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs Deposited 2026-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain QA 1–163（163 aa）
Chain QB 1–163（163 aa）
Chain QC 1–163（163 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
24MC Structure of oocyte cytoplasmic lattices Deposited 2026-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain h 1–163（163 aa）
Chain j 1–163（163 aa）
Chain l 1–163（163 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9W2M Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte Deposited 2025-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain K 1–163（163 aa）
Chain k 1–163（163 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9WSQ Structure of dimeric mouse NLRP14-KDM2A-SKP1 complex Deposited 2025-09-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–163（163 aa）
Chain F 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9XRL Structure of mouse cytoplasmic lattice (CPL) repeating unit Deposited 2025-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 73 PDB declaration: 73-meric
Chain D 1–163（163 aa）
Chain F 1–163（163 aa）
Chain O 1–163（163 aa）
Chain p 1–163（163 aa）
Chain q 1–163（163 aa）
Not recorded ZN ZINC ION × 13 GTP GUANOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.74 Å

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

View Construct and Data Evidence
UniProt name SKP1_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 12–174； UniProt 1–163

NACHT, LRR and PYD domains-containing protein 14

Mus musculus

UniProt Q6B966

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 1–993 Not recorded Lysine-specific demethylase 2A × 1 （P59997） S-phase kinase-associated protein 1 × 1 （Q9WTX5） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.79 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 9WSR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
12DL Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs Deposited 2026-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain DA 1–993（993 aa）
Chain DB 1–993（993 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
24MC Structure of oocyte cytoplasmic lattices Deposited 2026-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain e 1–993（993 aa）
Chain f 1–993（993 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9SFP Native cytoplasmic lattices from mouse oocytes Deposited 2025-08-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain J 1–993（993 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å
9W2M Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte Deposited 2025-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric
Chain N 28–993（966 aa）
Chain n 28–993（966 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9WSQ Structure of dimeric mouse NLRP14-KDM2A-SKP1 complex Deposited 2025-09-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–993（993 aa）
Chain D 1–993（993 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9XRL Structure of mouse cytoplasmic lattice (CPL) repeating unit Deposited 2025-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 73 PDB declaration: 73-meric
Chain AK 1–993（993 aa）
Chain AQ 1–993（993 aa）
Chain w 1–993（993 aa）
Not recorded ZN ZINC ION × 13 GTP GUANOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.74 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NAL14_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 21–1013； UniProt 1–993

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 9wsr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9wsr
Deposition date deposition_date2025-09-15
Structure title titleStructure of mouse NLRP14-KDM2A-SKP1 complex
Keywords keywordsCryo-EM, Complex, early embryonic development, NLRP14, KDM2A, SKP1, ubiquitylation., 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_guinier39.74 Å
Radius of gyration Rg (electron density) rg_electron39.07 Å
Forward intensity I(0) i0276838000.00
Molecular weight molecular_weight134470.0 kDa
Excluded volume excluded_volume168400 ų
Envelope volume envelope_volume244590 ų
Hydration-shell volume shell_volume52194 ų
Envelope diameter envelope_diameter119.9 Å
Shell Rg shell_rg44.92 Å
Envelope Rg envelope_rg38.08 Å
Shape Rg shape_rg39.10 Å
Total Rg total_rg39.33 Å
Total atoms total_atoms9408
Residues n_residues1192
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 dmax118.3 Å
Rg (real space) rg_real39.52 Å
Rg uncertainty (real space) rg_real_error0.99 Å
I(0) (real space) i0_real2.7680e+08
I(0) uncertainty (real space) i0_real_error5.3500e+06
Rg (reciprocal space) rg_reciprocal39.66 Å
I(0) (reciprocal space) i0_reciprocal276900000.0000
Solution quality estimate total_estimate0.9105
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary53.2 Å
Skewness Skewness skewness0.033
Kurtosis Kurtosis kurtosis-0.784
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33970000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.985; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.878
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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)