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6ig9

Tra1 subunit from Saccharomyces cerevisiae SAGA complex

Method: ELECTRON MICROSCOPY Dmax: 199.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription-associated protein 1

OrganismNot specified

UniProt P38811

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 T； UniProt 1–3744 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8.5；20mM HEPES pH 8.5 150mM Nacl cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds and wait for 30 seconds before plunging Resolution 4.60 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.

Other PDB Difference from Current Entry 6IG9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5OJS Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 Deposited 2017-07-24 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain T 1–3744（3744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Two subsequent applications of protein were required to achieve the desired particle density on grids. Each application was followed by 20 sec waiting time, with a short 0.5 sec blotting after first application and 5 sec blotting after the second.
Resolution 3.70 Å
5Y81 NuA4 TEEAA sub-complex Deposited 2017-08-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–2627（2627 aa） Fragment：UNP residues 1-2627
Chain B 2630–3744（1115 aa） Fragment：UNP residues 2630-3744
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain T 1–3744（3744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å
6T9J SAGA Tra1 module Deposited 2019-10-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain T 1–3744（3744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.40 Å
7VVY TRA module of NuA4 Deposited 2021-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 1–3744（3744 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain L 1–3744（3744 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.80 Å
7YFN Core module of the NuA4 complex in S. cerevisiae Deposited 2022-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain T 1–3744（3744 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7YFP The NuA4 histone acetyltransferase complex from S. cerevisiae Deposited 2022-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain T 1–3744（3744 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8ESC Structure of the Yeast NuA4 Histone Acetyltransferase Complex Deposited 2022-10-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Z 1–3744（3744 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRA1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain T； PDBConstruct 1–3744； UniProt 1–3744

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 6ig9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ig9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ig9
Deposition date deposition_date2018-09-25
Structure title titleTra1 subunit from Saccharomyces cerevisiae SAGA complex
Keywords keywordsEpigenetics, Acetyltransferase, Transcription, Co-activator; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier58.81 Å
Radius of gyration Rg (electron density) rg_electron58.89 Å
Forward intensity I(0) i01164140000.00
Molecular weight molecular_weight239460.0 kDa
Excluded volume excluded_volume278890 ų
Envelope volume envelope_volume669540 ų
Hydration-shell volume shell_volume95576 ų
Envelope diameter envelope_diameter195.1 Å
Shell Rg shell_rg62.40 Å
Envelope Rg envelope_rg55.85 Å
Shape Rg shape_rg58.89 Å
Total Rg total_rg59.00 Å
Total atoms total_atoms17122
Residues n_residues3386
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 dmax199.3 Å
Rg (real space) rg_real58.85 Å
Rg uncertainty (real space) rg_real_error1.78 Å
I(0) (real space) i0_real1.1640e+09
I(0) uncertainty (real space) i0_real_error2.3220e+07
Rg (reciprocal space) rg_reciprocal58.76 Å
I(0) (reciprocal space) i0_reciprocal1164000000.0000
Solution quality estimate total_estimate0.5916
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.5 Å
Skewness Skewness skewness0.300
Kurtosis Kurtosis kurtosis-0.488
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0004
Highest regularization parameter α highest_alpha125100000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)