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4e4h

Crystal structure of Histone Demethylase NO66

Method: X-RAY DIFFRACTION Dmax: 123.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific demethylase NO66

Homo sapiens

UniProt Q9H6W3

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 183–641 Chain B； UniProt 183–641 Chain C； UniProt 183–641 Chain D； UniProt 183–641 Fragment：UNP RESIDUES 183-641 FE FE (III) ION × 4 ACT ACETATE ION × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；200mM (NH4)2SO4, 100mM Tris-HCl, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.28 Å R-free 0.252

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 4E4H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4CCJ 60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form Deposited 2013-10-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain C 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain D 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Mutation：YES Mutation：YES Mutation：YES Mutation：YES EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；NAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 5.6-6.5, 0.5-0.7M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.15 Å R-free 0.210
4CCK 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and N-oxalylglycine (NOG) Deposited 2013-10-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain C 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain D 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Mutation：YES Mutation：YES Mutation：YES Mutation：YES MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 5.6-6.5, 0.5-0.7M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.15 Å R-free 0.197
4CCM 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1) Deposited 2013-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Not recorded MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M BIS-TRIS PROPANE PH 6.8, 0.25M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K VAPOR DIFFUSION, SITTING DROP
Resolution 2.51 Å R-free 0.236
4CCN 60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-2) Deposited 2013-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Not recorded MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 7.4, 0.4M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.23 Å R-free 0.248
4CCO 60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G214C) peptide fragment (complex-3) Deposited 2013-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Not recorded MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 7.4, 0.36M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.30 Å R-free 0.225
4DIQ Crystal Structure of human NO66 Deposited 2012-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 167–641（475 aa） Fragment：UNP residues 161-641
Chain B 167–641（475 aa） Fragment：UNP residues 161-641
Not recorded NI NICKEL (II) ION × 2 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05M (NH4)2SO4, 0.05M BIS-TRIS pH 6.5, 30% pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.230
4DIQ Crystal Structure of human NO66 Deposited 2012-01-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 167–641（475 aa） Fragment：UNP residues 161-641
Chain B 167–641（475 aa） Fragment：UNP residues 161-641
Not recorded NI NICKEL (II) ION × 4 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05M (NH4)2SO4, 0.05M BIS-TRIS pH 6.5, 30% pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.230
4Y33 Crystal of NO66 in complex with Ni(II)and N-oxalylglycine (NOG) Deposited 2015-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain B 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain C 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain D 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Not recorded NI NICKEL (II) ION × 4 OGA N-OXALYLGLYCINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；15%(v/v) ethanol, imidazole pH8.0, 0.2M magnesium chloride
Resolution 2.70 Å R-free 0.274
4Y3O Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine Deposited 2015-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain B 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Not recorded NI NICKEL (II) ION × 2 OGA N-OXALYLGLYCINE × 2 GOL GLYCEROL × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M Imidazole pH 6.5, 0.5 M Sodium acetate trihydrate
Resolution 2.20 Å R-free 0.262
4Y4R Crystal structure of ribosomal oxygenase NO66 dimer mutant Deposited 2015-02-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 176–525（350 aa） Fragment：UNP RESIDUES 176-525, 541-641
Chain A 541–641（101 aa） Fragment：UNP RESIDUES 176-525, 541-641
Chain B 176–525（350 aa） Fragment：UNP RESIDUES 176-525, 541-641
Chain B 541–641（101 aa） Fragment：UNP RESIDUES 176-525, 541-641
Not recorded NI NICKEL (II) ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.0M ammonium monohydric phosphate, 0.1M acetate pH4.5
Resolution 3.30 Å R-free 0.271

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NO66_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–463； UniProt 183–641 Author chain B； PDBConstruct 5–463； UniProt 183–641 Author chain C； PDBConstruct 5–463； UniProt 183–641 Author chain D； PDBConstruct 5–463； UniProt 183–641

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 4e4h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4e4h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4e4h
Deposition date deposition_date2012-03-13
Structure title titleCrystal structure of Histone Demethylase NO66
Keywords keywordsJmjc domain, wHTH domain, Histone Demethylase, OXIDOREDUCTASE; 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_guinier43.14 Å
Radius of gyration Rg (electron density) rg_electron42.29 Å
Forward intensity I(0) i0643688000.00
Molecular weight molecular_weight207870.0 kDa
Excluded volume excluded_volume259570 ų
Envelope volume envelope_volume376080 ų
Hydration-shell volume shell_volume71927 ų
Envelope diameter envelope_diameter120.8 Å
Shell Rg shell_rg51.15 Å
Envelope Rg envelope_rg39.63 Å
Shape Rg shape_rg42.28 Å
Total Rg total_rg42.76 Å
Total atoms total_atoms14662
Residues n_residues1825
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 dmax123.0 Å
Rg (real space) rg_real42.80 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real6.4370e+08
I(0) uncertainty (real space) i0_real_error1.0400e+07
Rg (reciprocal space) rg_reciprocal43.13 Å
I(0) (reciprocal space) i0_reciprocal643900000.0000
Solution quality estimate total_estimate0.8872
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary66.5 Å
Skewness Skewness skewness-0.144
Kurtosis Kurtosis kurtosis-0.718
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha120000000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.740
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id4e4hA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4e4hA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain
Domain ID domain_id4e4hA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4e4hB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4e4hB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain
Domain ID domain_id4e4hB03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4e4hC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4e4hC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain
Domain ID domain_id4e4hC03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4e4hD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4e4hD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain
Domain ID domain_id4e4hD03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)