4uus

CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF

Method: X-RAY DIFFRACTION Dmax: 88.2 Å Quality: GOOD

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

HOMEOTIC PROTEIN ULTRABITHORAX

DROSOPHILA MELANOGASTER

UniProt P83949

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–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 292–367 Fragment:HOMEODOMAIN AND UBDA, RESIDUES 292-367 Mutation:YES HOMEOTIC PROTEIN EXTRADENTICLE × 1 (P40427) 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3' × 1 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.5;0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000 Resolution 2.55 Å R-free 0.239
2 Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain E; UniProt 292–367 Fragment:HOMEODOMAIN AND UBDA, RESIDUES 292-367 Mutation:YES HOMEOTIC PROTEIN EXTRADENTICLE × 1 (P40427) 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3' × 1 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.5;0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000 Resolution 2.55 Å R-free 0.239

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.

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

View Construct and Data Evidence
UniProt name UBX_DROME
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–77; UniProt 292–367 Author chain E; PDBConstruct 2–77; UniProt 292–367

HOMEOTIC PROTEIN EXTRADENTICLE

DROSOPHILA MELANOGASTER

UniProt P40427

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–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain B; UniProt 238–312 Fragment:HOMEODOMAIN RESIDUES 238-312 HOMEOTIC PROTEIN ULTRABITHORAX × 1 (P83949) 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3' × 1 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.5;0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000 Resolution 2.55 Å R-free 0.239
2 Protein–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain F; UniProt 238–312 Fragment:HOMEODOMAIN RESIDUES 238-312 HOMEOTIC PROTEIN ULTRABITHORAX × 1 (P83949) 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3' × 1 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.5;0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000 Resolution 2.55 Å R-free 0.239

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.

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

View Construct and Data Evidence
UniProt name EXD_DROME
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–76; UniProt 238–312 Author chain F; PDBConstruct 2–76; UniProt 238–312

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 4uus

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4uus
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4uus
Deposition date deposition_date2014-07-31
Structure title titleCRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF
Keywords keywordsTRANSCRIPTION, HOMEODOMAIN, HOX PROTEIN, PBC PROTEIN, DNA PROTEIN COMPLEX, TRANSCRIPTION FACTOR; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.94
Radius of gyration Rg (electron density) rg_electron26.53
Forward intensity I(0) i064944300.00
Molecular weight molecular_weight50561.0 kDa
Excluded volume excluded_volume58040 ų
Envelope volume envelope_volume81982 ų
Hydration-shell volume shell_volume26697 ų
Envelope diameter envelope_diameter95.0
Shell Rg shell_rg32.70
Envelope Rg envelope_rg26.23
Shape Rg shape_rg26.52
Total Rg total_rg27.16
Total atoms total_atoms3492
Residues n_residues321
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax88.2
Rg (real space) rg_real26.96
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real6.4940e+07
I(0) uncertainty (real space) i0_real_error9.6090e+05
Rg (reciprocal space) rg_reciprocal26.96
I(0) (reciprocal space) i0_reciprocal64940000.0000
Solution quality estimate total_estimate0.8194
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary86.7
Skewness Skewness skewness0.309
Kurtosis Kurtosis kurtosis-0.480
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7803000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4uusA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4uusB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4uusE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4uusF00
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)