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6i9h

Solution structure of TRIM28 RING domain

Method: SOLUTION NMR Dmax: 38.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 54–145 Not recorded ZN ZINC ION × 2 SOLUTION NMR NMR measurement conditions：pH 6.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR measurement conditions：pH 6.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：1 mM [U-15N] TRIM28 RING, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-13C; U-15N] TRIM28 RING, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 6I9H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FP0 SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR Deposited 2000-08-29 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 619–679（61 aa） Fragment：PHD DOMAIN
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；303 K；Pressure AMBIENT
NMR sample composition 1.5-3.0 mM 15N-labelled or unlabelled KAP-1 PHD, 20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.5 | 90% H2O/10% D2O
NMR sample composition 1.5-3.0 mM unlabelled KAP-1 PHD, 20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.5 | 100% D2O
Resolution not provided
2RO1 NMR Solution Structures of Human KAP1 PHD finger-bromodomain Deposited 2008-03-04 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 624–812（189 aa） Fragment：UNP residues 624-812
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient
NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] protein, 100% D2O | 100% D2O
Resolution not provided
2YVR Crystal structure of MS1043 Deposited 2007-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 201–250（50 aa） Fragment：zf-B_box domain, residues in database 201-250
Chain B 201–250（50 aa） Fragment：zf-B_box domain, residues in database 201-250
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；HEPES, PEG4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.218
6H3A Crystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain. Deposited 2018-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 53–434（382 aa）
Chain F 53–434（382 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.2 M Sodium Malonate, 0.5 % Jeffamine ED-2003 and 0.1 M HEPES pH 7.0
Resolution 5.50 Å R-free 0.303
6QAJ Structure of the tripartite motif of KAP1/TRIM28 Deposited 2018-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 56–413（358 aa）
Chain B 56–413（358 aa）
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
6QU1 Crystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain at 3.7 angstrom resolution. Deposited 2019-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 53–142（90 aa）
Chain A 203–434（232 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25 % PEG 3350, 0.1 M HEPES pH 7.5
Resolution 3.70 Å R-free 0.346
7Z36 Crystal structure of the KAP1 tripartite motif in complex with the ZNF93 KRAB domain Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 56–140（85 aa）
Chain B 56–140（85 aa）
Mutation：KAP1 B-box 1 domain (residues 141-202) deleted Mutation：KAP1 B-box 1 domain (residues 141-202) deleted ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；11% (w/v) PEG 5000 MME 5% Tacsimate 0.1 M HEPES pH 7
Resolution 2.80 Å R-free 0.274
9CDW Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide Deposited 2024-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 485–490（6 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine
Resolution 2.40 Å R-free 0.252
9CDW Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide Deposited 2024-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 485–490（6 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine
Resolution 2.40 Å R-free 0.252
9OSC Crystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide Deposited 2025-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 483–493（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M LiCl2, 0.1 M citrate buffer pH 4.0, and 20% PEG6000
Resolution 1.77 Å R-free 0.236

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 3–94； UniProt 54–145

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 6i9h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6i9h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6i9h
Deposition date deposition_date2018-11-23
Structure title titleSolution structure of TRIM28 RING domain
Keywords keywordsTRIM, E3 ligase, enzyme, ubiquitin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.16 Å
Radius of gyration Rg (electron density) rg_electron13.97 Å
Forward intensity I(0) i0540878000.00
Molecular weight molecular_weight173460.0 kDa
Excluded volume excluded_volume207660 ų
Envelope volume envelope_volume30992 ų
Hydration-shell volume shell_volume14678 ų
Envelope diameter envelope_diameter69.2 Å
Shell Rg shell_rg24.07 Å
Envelope Rg envelope_rg19.49 Å
Shape Rg shape_rg14.05 Å
Total Rg total_rg13.97 Å
Total atoms total_atoms23130
Residues n_residues1656
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax38.6 Å
Rg (real space) rg_real13.32 Å
Rg uncertainty (real space) rg_real_error0.07 Å
I(0) (real space) i0_real5.1630e+08
I(0) uncertainty (real space) i0_real_error4.7480e+06
Rg (reciprocal space) rg_reciprocal14.34 Å
I(0) (reciprocal space) i0_reciprocal540900000.0000
Solution quality estimate total_estimate0.6702
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary14.7 Å
Skewness Skewness skewness0.391
Kurtosis Kurtosis kurtosis-0.285
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.6020
Highest regularization parameter α highest_alpha272100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.923; Stabil: 0.982; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)