9cad

Cryo-EM structure of the TRRAP lobe of the native human TIP60 complex (composite structure)

Method: ELECTRON MICROSCOPY Dmax: 204.9 Å Quality: GOOD

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

E1A-binding protein p400

OrganismNot specified

UniProt Q96L91

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 A; UniProt 1–3159 Not recorded Isoform 2 of Transformation/transcription domain-associated protein × 1 (Q9Y4A5) IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.05 Å

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EP400_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–3159; UniProt 1–3159

Isoform 2 of Transformation/transcription domain-associated protein

OrganismNot specified

UniProt Q9Y4A5

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 D; UniProt 1–3830 Not recorded E1A-binding protein p400 × 1 (Q96L91) IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.05 Å

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRRAP_HUMAN
Isoform Q9Y4A5-2
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–3830; UniProt 1–3830

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 9cad

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cad
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cad
Deposition date deposition_date2024-06-17
Structure title titleCryo-EM structure of the TRRAP lobe of the native human TIP60 complex (composite structure)
Keywords keywordshistone acetyltransferase, chromatin regulator, transcription regulation, GENE REGULATION; GENE REGULATION
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier58.94
Radius of gyration Rg (electron density) rg_electron58.74
Forward intensity I(0) i02425640000.00
Molecular weight molecular_weight426040.0 kDa
Excluded volume excluded_volume538270 ų
Envelope volume envelope_volume806990 ų
Hydration-shell volume shell_volume112010 ų
Envelope diameter envelope_diameter203.6
Shell Rg shell_rg64.48
Envelope Rg envelope_rg57.18
Shape Rg shape_rg58.76
Total Rg total_rg58.80
Total atoms total_atoms29915
Residues n_residues3723
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 dmax204.9
Rg (real space) rg_real58.99
Rg uncertainty (real space) rg_real_error2.09
I(0) (real space) i0_real2.4260e+09
I(0) uncertainty (real space) i0_real_error5.1880e+07
Rg (reciprocal space) rg_reciprocal58.87
I(0) (reciprocal space) i0_reciprocal2425000000.0000
Solution quality estimate total_estimate0.8719
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary68.3
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.464
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha0.0004
Highest regularization parameter α highest_alpha202100000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.806

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)