← Back to search
1q1v

Structure of the Oncoprotein DEK: a putative DNA-binding Domain Related to the Winged Helix Motif

Method: SOLUTION NMR Dmax: 39.9 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

DEK protein

Homo sapiens

UniProt P35659

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 309–375 Fragment：RESIDUES 309-378 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.75；293 K；Ionic strength (raw mmCIF value) 50mM NAPO4, 100mM KCL；Pressure AMBIENT NMR sample composition：1.0MM DEK C-TERMINAL DOMAIN Resolution not provided

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 1Q1V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2JX3 NMR solution structure of the N-terminal domain of DEK Deposited 2007-11-02 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 78–208（131 aa） Fragment：SAP domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100mM KCL；Pressure ambient
NMR sample composition 0.65 mM [U-100% 13C; U-100% 15N] DEK78-208, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain K 1–375（375 aa）
Chain L 1–375（375 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–375（375 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–375（375 aa）
Chain L 1–375（375 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–375（375 aa）
Chain L 1–375（375 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name DEK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–67； UniProt 309–375

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 1q1v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1q1v
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1q1v
Deposition date deposition_date2003-07-22
Structure title titleStructure of the Oncoprotein DEK: a putative DNA-binding Domain Related to the Winged Helix Motif
Keywords keywordsWINGED-HELIX MOTIF, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.23 Å
Radius of gyration Rg (electron density) rg_electron14.11 Å
Forward intensity I(0) i086147000.00
Molecular weight molecular_weight82507.0 kDa
Excluded volume excluded_volume105900 ų
Envelope volume envelope_volume27873 ų
Hydration-shell volume shell_volume13524 ų
Envelope diameter envelope_diameter62.4 Å
Shell Rg shell_rg24.25 Å
Envelope Rg envelope_rg20.24 Å
Shape Rg shape_rg14.10 Å
Total Rg total_rg14.73 Å
Total atoms total_atoms11940
Residues n_residues700
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax39.9 Å
Rg (real space) rg_real13.17 Å
Rg uncertainty (real space) rg_real_error0.08 Å
I(0) (real space) i0_real8.2140e+07
I(0) uncertainty (real space) i0_real_error6.9460e+05
Rg (reciprocal space) rg_reciprocal14.55 Å
I(0) (reciprocal space) i0_reciprocal86150000.0000
Solution quality estimate total_estimate0.6202
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary14.6 Å
Skewness Skewness skewness0.460
Kurtosis Kurtosis kurtosis-0.024
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha2.9000
Highest regularization parameter α highest_alpha166200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.007; Oscil: 0.711; Stabil: 0.979; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1q1va1
Class classa — All alpha proteins
Fold Fold folda.159 — Another 3-helical bundle
Superfamily Superfamily superfamilya.159.4 — DEK C-terminal domain
Family Family familya.159.4.1 — DEK C-terminal domain
Domain ID domain_idd1q1va2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1q1vA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
▶

8. Citations (1)

▶

9. Files and Curves (10)