6qaj

Structure of the tripartite motif of KAP1/TRIM28

Method: X-RAY DIFFRACTION Dmax: 192.0 Å Quality: REASONABLE

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

Endolysin,Transcription intermediary factor 1-beta

Homo sapiens

UniProt P00720

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–161 Chain B; UniProt 2–161 Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;291 K;15% (w/v) PEG 3350, 75 mM MgCl2, 0.1 M HEPES pH 7.5 Resolution 2.90 Å R-free 0.291

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.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 26–185; UniProt 2–161 Author chain B; PDBConstruct 26–185; UniProt 2–161

Endolysin,Transcription intermediary factor 1-beta

Homo sapiens

UniProt Q13263

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 56–413 Chain B; UniProt 56–413 Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;291 K;15% (w/v) PEG 3350, 75 mM MgCl2, 0.1 M HEPES pH 7.5 Resolution 2.90 Å R-free 0.291

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 TIF1B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 187–544; UniProt 56–413 Author chain B; PDBConstruct 187–544; UniProt 56–413

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 6qaj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6qaj
Deposition date deposition_date2018-12-19
Structure title titleStructure of the tripartite motif of KAP1/TRIM28
Keywords keywords;Transcriptional repressor; epigenetic silencing; histone H3 lysine 9 methylation (H3K9me3); endogenous retrovirus; retrotransposon; transposable element; tripartite motif (TRIM); SUMO; ubiquitin; E3 ligase, NUCLEAR PROTEIN ;; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier57.08
Radius of gyration Rg (electron density) rg_electron57.55
Forward intensity I(0) i0154625000.00
Molecular weight molecular_weight99752.0 kDa
Excluded volume excluded_volume123630 ų
Envelope volume envelope_volume222690 ų
Hydration-shell volume shell_volume35029 ų
Envelope diameter envelope_diameter199.8
Shell Rg shell_rg54.45
Envelope Rg envelope_rg54.78
Shape Rg shape_rg57.48
Total Rg total_rg57.68
Total atoms total_atoms13867
Residues n_residues880
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 dmax192.0
Rg (real space) rg_real57.99
Rg uncertainty (real space) rg_real_error2.86
I(0) (real space) i0_real1.5460e+08
I(0) uncertainty (real space) i0_real_error3.4920e+06
Rg (reciprocal space) rg_reciprocal56.27
I(0) (reciprocal space) i0_reciprocal154200000.0000
Solution quality estimate total_estimate0.6343
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3
Skewness Skewness skewness0.441
Kurtosis Kurtosis kurtosis-0.803
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6003000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.284; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.155; Smooth: 0.235

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)