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4do0

Crystal Structure of human PHF8 in complex with Daminozide

Method: X-RAY DIFFRACTION Dmax: 70.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone lysine demethylase PHF8

Homo sapiens

UniProt Q9UPP1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 115–483 Not recorded DZA DAMINOZIDE × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 12 EDO 1,2-ETHANEDIOL × 6 ACT ACETATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；277 K；0.1M acetate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, temperature 277K Resolution 2.55 Å R-free 0.265

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 4DO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2WWU Crystal structure of the catalytic domain of PHD finger protein 8 Deposited 2009-10-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 115–483（369 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 115-483
Not recorded SO4 SULFATE ION × 14 ACT ACETATE ION × 10 NI NICKEL (II) ION × 2 BGC beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions 1.5 M (NH4)2SO4, 0.1 M SODIUM ACETATE PH 4.25
Resolution 2.15 Å R-free 0.211
3KV4 Structure of PHF8 in complex with histone H3 Deposited 2009-11-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–483（447 aa） Fragment：UNP Residues 37-483
Not recorded ZN ZINC ION × 2 FE2 FE (II) ION × 1 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 13 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；25% (v/v) polyethylene glycol 3350, 0.2 M NaCl, and 0.1 M NaCitrate pH 5.6, VAPOR DIFFUSION, HANGING DROP
Resolution 2.19 Å R-free 0.255
7CMZ Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8 Deposited 2020-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 842–863（22 aa）
Not recorded K POTASSIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic
Resolution 1.70 Å R-free 0.215

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

View Construct and Data Evidence
UniProt name PHF8_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–374； UniProt 115–483

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 4do0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4do0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4do0
Deposition date deposition_date2012-02-09
Structure title titleCrystal Structure of human PHF8 in complex with Daminozide
Keywords keywords;JMJC DOMAIN, METAL BINDING PROTEIN, Histone demethylase, Epigenetics, Daminozide, Structural Genomics, Structural Genomics Consortium, SGC ;; METAL BINDING PROTEIN
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_guinier22.40 Å
Radius of gyration Rg (electron density) rg_electron21.15 Å
Forward intensity I(0) i029536900.00
Molecular weight molecular_weight41807.0 kDa
Excluded volume excluded_volume52281 ų
Envelope volume envelope_volume62283 ų
Hydration-shell volume shell_volume24375 ų
Envelope diameter envelope_diameter72.6 Å
Shell Rg shell_rg28.16 Å
Envelope Rg envelope_rg21.43 Å
Shape Rg shape_rg21.12 Å
Total Rg total_rg22.12 Å
Total atoms total_atoms2937
Residues n_residues363
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 dmax70.5 Å
Rg (real space) rg_real22.33 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real2.9540e+07
I(0) uncertainty (real space) i0_real_error3.2180e+05
Rg (reciprocal space) rg_reciprocal22.35 Å
I(0) (reciprocal space) i0_reciprocal29540000.0000
Solution quality estimate total_estimate0.9002
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7 Å
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.329
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9986000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4do0a_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.2 — Clavaminate synthase-like
Family Family familyb.82.2.14 — Jumonji domain / Histone demethylase core

CATH v4.4 (2 domains)

Domain ID domain_id4do0A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4do0A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1360 —
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8. Citations (0)

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9. Files and Curves (10)