6dnq

HBZ77 in complex with KIX and c-Myb

Method: X-RAY DIFFRACTION Dmax: 91.7 Å Quality: GOOD

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

BZIP factor

Human T-lymphotropic virus 1

UniProt Q2Q067

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 3–77 Fragment:residues 3-77 Transcriptional activator Myb × 2 (P06876) CREB-binding protein × 2 (P45481) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;PEG 3350, calcium chloride Resolution 2.35 Å R-free 0.229

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.

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q2Q067_9DELA
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 5–79; UniProt 3–77

Transcriptional activator Myb

Mus musculus

UniProt P06876

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 284–315 Chain C; UniProt 284–315 Fragment:residues 284-315 BZIP factor × 1 (Q2Q067) CREB-binding protein × 2 (P45481) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;PEG 3350, calcium chloride Resolution 2.35 Å R-free 0.229

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.

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYB_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–32; UniProt 284–315 Author chain C; PDBConstruct 1–32; UniProt 284–315

CREB-binding protein

Mus musculus

UniProt P45481

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 586–672 Chain D; UniProt 586–672 Fragment:residues 586-672 BZIP factor × 1 (Q2Q067) Transcriptional activator Myb × 2 (P06876) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;PEG 3350, calcium chloride Resolution 2.35 Å R-free 0.229

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.

23 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBP_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 2–88; UniProt 586–672 Author chain D; PDBConstruct 2–88; UniProt 586–672

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 6dnq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dnq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dnq
Deposition date deposition_date2018-06-07
Structure title titleHBZ77 in complex with KIX and c-Myb
Keywords keywordstranscription coactivator, transcription factor, viral, eukaryotic, complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.76
Radius of gyration Rg (electron density) rg_electron26.31
Forward intensity I(0) i017696000.00
Molecular weight molecular_weight31915.0 kDa
Excluded volume excluded_volume40027 ų
Envelope volume envelope_volume54336 ų
Hydration-shell volume shell_volume18722 ų
Envelope diameter envelope_diameter95.8
Shell Rg shell_rg30.97
Envelope Rg envelope_rg26.31
Shape Rg shape_rg26.33
Total Rg total_rg26.87
Total atoms total_atoms4483
Residues n_residues278
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 dmax91.7
Rg (real space) rg_real26.94
Rg uncertainty (real space) rg_real_error0.91
I(0) (real space) i0_real1.7700e+07
I(0) uncertainty (real space) i0_real_error2.5610e+05
Rg (reciprocal space) rg_reciprocal26.89
I(0) (reciprocal space) i0_reciprocal17700000.0000
Solution quality estimate total_estimate0.8442
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9
Skewness Skewness skewness0.390
Kurtosis Kurtosis kurtosis-0.604
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1689000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.634; Smooth: 0.965

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_idd6dnqb_
Class classa — All alpha proteins
Fold Fold folda.12 — Kix domain of CBP (creb binding protein)
Superfamily Superfamily superfamilya.12.1 — Kix domain of CBP (creb binding protein)
Family Family familya.12.1.1 — Kix domain of CBP (creb binding protein)
Domain ID domain_idd6dnqd_
Class classa — All alpha proteins
Fold Fold folda.12 — Kix domain of CBP (creb binding protein)
Superfamily Superfamily superfamilya.12.1 — Kix domain of CBP (creb binding protein)
Family Family familya.12.1.1 — Kix domain of CBP (creb binding protein)

CATH v4.4 (2 domains)

Domain ID domain_id6dnqB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily20 — Coactivator CBP, KIX domain
Domain ID domain_id6dnqD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily20 — Coactivator CBP, KIX domain

8. Citations (1)

9. Files and Curves (10)