6toq

Crystal structure of a PP2A B56y/HTLV-1 integrase complex

Method: X-RAY DIFFRACTION Dmax: 89.3 Å Quality: GOOD

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

Pol protein

Human T-cell leukemia virus type I

UniProt A0A1Y1CAL3

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain CCC; UniProt 766–863 Not recorded Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform × 1 (Q13362) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293.15 K;0.1 M Na/KPO4 pH 6.2, 20-% 1,2-propanediol, 10% glycerol Resolution 3.16 Å R-free 0.294

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A1Y1CAL3_9DELA
Isoform
PDB entities 1
Chains and sequence ranges Author chain CCC; PDBConstruct 1–98; UniProt 766–863

Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform

Homo sapiens

UniProt Q13362

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain AAA; UniProt 11–380 Not recorded Pol protein × 1 (A0A1Y1CAL3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293.15 K;0.1 M Na/KPO4 pH 6.2, 20-% 1,2-propanediol, 10% glycerol Resolution 3.16 Å R-free 0.294

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.

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

View Construct and Data Evidence
UniProt name 2A5G_HUMAN
Isoform Q13362-3
PDB entities 2
Chains and sequence ranges Author chain AAA; PDBConstruct 1–370; UniProt 11–380

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 6toq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6toq
Deposition date deposition_date2019-12-11
Structure title titleCrystal structure of a PP2A B56y/HTLV-1 integrase complex
Keywords keywordsPhosphatase, integrase, complex, SLiM, dephosphorylation, cell signalling, motif mimicry, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.41
Radius of gyration Rg (electron density) rg_electron24.81
Forward intensity I(0) i020667800.00
Molecular weight molecular_weight37784.0 kDa
Excluded volume excluded_volume48548 ų
Envelope volume envelope_volume58418 ų
Hydration-shell volume shell_volume21153 ų
Envelope diameter envelope_diameter90.9
Shell Rg shell_rg30.28
Envelope Rg envelope_rg24.93
Shape Rg shape_rg24.77
Total Rg total_rg25.65
Total atoms total_atoms2674
Residues n_residues336
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 dmax89.3
Rg (real space) rg_real25.59
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real2.0670e+07
I(0) uncertainty (real space) i0_real_error3.0250e+05
Rg (reciprocal space) rg_reciprocal25.54
I(0) (reciprocal space) i0_reciprocal20670000.0000
Solution quality estimate total_estimate0.8295
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1
Skewness Skewness skewness0.508
Kurtosis Kurtosis kurtosis-0.350
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6253000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.681; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.749; Smooth: 0.988

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)