1b8i

STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX

Method: X-RAY DIFFRACTION Dmax: 60.7 Å Quality: GOOD

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

PROTEIN (ULTRABITHORAX HOMEOTIC PROTEIN IV)

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 233–313 Fragment:YPWM MOTIF AND HOMEODOMAIN Mutation:C139S ;DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3') ; × 1 ;DNA (5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3') ; × 1 PROTEIN (HOMEOBOX PROTEIN EXTRADENTICLE) × 1 (P40427) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;0.6M AMMONIUM PHOSPHATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP Resolution 2.40 Å R-free 0.304

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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBX_DROME
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–81; UniProt 233–313

PROTEIN (HOMEOBOX 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 238–300 Fragment:HOMEODOMAIN ;DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3') ; × 1 ;DNA (5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3') ; × 1 PROTEIN (ULTRABITHORAX HOMEOTIC PROTEIN IV) × 1 (P83949) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;0.6M AMMONIUM PHOSPHATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP Resolution 2.40 Å R-free 0.304

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 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EXD_DROME
Isoform
PDB entities 4
Chains and sequence ranges Author chain B; PDBConstruct 1–63; UniProt 238–300

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 1b8i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b8i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b8i
Deposition date deposition_date1999-02-01
Structure title titleSTRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX
Keywords keywordsDNA BINDING, HOMEODOMAIN, HOMEOTIC PROTEINS, DEVELOPMENT, SPECIFICITY, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.38
Radius of gyration Rg (electron density) rg_electron18.04
Forward intensity I(0) i015346000.00
Molecular weight molecular_weight23715.0 kDa
Excluded volume excluded_volume27131 ų
Envelope volume envelope_volume33430 ų
Hydration-shell volume shell_volume16086 ų
Envelope diameter envelope_diameter62.3
Shell Rg shell_rg23.33
Envelope Rg envelope_rg18.13
Shape Rg shape_rg18.04
Total Rg total_rg18.72
Total atoms total_atoms1637
Residues n_residues150
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 dmax60.7
Rg (real space) rg_real18.35
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real1.5350e+07
I(0) uncertainty (real space) i0_real_error1.8640e+05
Rg (reciprocal space) rg_reciprocal18.36
I(0) (reciprocal space) i0_reciprocal15350000.0000
Solution quality estimate total_estimate0.8889
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.1
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.282
Angular range angular_range— – 0.4350 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha1998000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1b8ia_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.1 — Homeodomain
Domain ID domain_idd1b8ib_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.1 — Homeodomain

CATH v4.4 (2 domains)

Domain ID domain_id1b8iA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id1b8iB00
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)