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4bbq

Crystal structure of the CXXC and PHD domain of Human Lysine-specific Demethylase 2A (KDM2A)(FBXL11)

Method: X-RAY DIFFRACTION Dmax: 90.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LYSINE-SPECIFIC DEMETHYLASE 2A

HOMO SAPIENS

UniProt Q9Y2K7

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 567–681 Fragment：CXXC AND PHD DOMAIN, RESIDUES 567-681 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.1M BIS-TRIS, PH 6.5, 20%(W/V) PEG METHYL ETHER 5000 Resolution 2.24 Å R-free 0.221
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 567–681 Fragment：CXXC AND PHD DOMAIN, RESIDUES 567-681 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.1M BIS-TRIS, PH 6.5, 20%(W/V) PEG METHYL ETHER 5000 Resolution 2.24 Å R-free 0.221

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 4BBQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2YU1 Crystal structure of hJHDM1A complexed with a-ketoglutarate Deposited 2007-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–383（383 aa） Fragment：residues 1-383, residues 450-517
Chain A 450–517（68 aa） Fragment：residues 1-383, residues 450-517
Mutation：K252S Mutation：K252S FE2 FE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25% PEG 3350, 0.1M NaCl, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.273
2YU2 Crystal structure of hJHDM1A without a-ketoglutarate Deposited 2007-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–383（383 aa） Fragment：residues 1-383, residues 450-517
Chain A 450–517（68 aa） Fragment：residues 1-383, residues 450-517
Mutation：K252S Mutation：K252S FE2 FE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25% PEG 3350, 0.1M NaCl, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.70 Å R-free 0.287
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 888–932（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 888–932（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 888–932（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 888–932（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 888–932（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
7UV9 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Deposited 2022-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 2–685（684 aa）
Not recorded OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KDM2A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–117； UniProt 567–681 Author chain B； PDBConstruct 3–117； UniProt 567–681

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 4bbq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4bbq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4bbq
Deposition date deposition_date2012-09-27
Structure title titleCrystal structure of the CXXC and PHD domain of Human Lysine-specific Demethylase 2A (KDM2A)(FBXL11)
Keywords keywordsOXIDOREDUCTASE, UBIQUITIN, LIGASE, UBIQUITINATION, DEMETHYLATION, ZF-CXXC DNA BINDING DOMAIN, CPG ISLAND, CHROMATIN, KDM2A, FBXL11; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.33 Å
Radius of gyration Rg (electron density) rg_electron27.39 Å
Forward intensity I(0) i011965400.00
Molecular weight molecular_weight23447.0 kDa
Excluded volume excluded_volume28058 ų
Envelope volume envelope_volume42778 ų
Hydration-shell volume shell_volume14594 ų
Envelope diameter envelope_diameter94.2 Å
Shell Rg shell_rg30.88 Å
Envelope Rg envelope_rg26.63 Å
Shape Rg shape_rg27.45 Å
Total Rg total_rg27.63 Å
Total atoms total_atoms1576
Residues n_residues217
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 dmax90.8 Å
Rg (real space) rg_real27.60 Å
Rg uncertainty (real space) rg_real_error0.93 Å
I(0) (real space) i0_real1.1970e+07
I(0) uncertainty (real space) i0_real_error1.7320e+05
Rg (reciprocal space) rg_reciprocal27.52 Å
I(0) (reciprocal space) i0_reciprocal11960000.0000
Solution quality estimate total_estimate0.7959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary39.1 Å
Skewness Skewness skewness0.367
Kurtosis Kurtosis kurtosis-0.389
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha349800.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.661; Smooth: 0.754
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4bbqA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id4bbqB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (10)