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6t9j

SAGA Tra1 module

Method: ELECTRON MICROSCOPY Dmax: 205.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription factor SPT20

Saccharomyces cerevisiae S288C

UniProt P50875

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–604 Not recorded Transcription initiation factor TFIID subunit 12 × 1 （Q03761） Transcription-associated protein 1 × 1 （P38811） 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

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 6T9J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–604（604 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
6T9K SAGA Core module Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–604（604 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 3.30 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPT20_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–604； UniProt 1–604

Transcription initiation factor TFIID subunit 12

Saccharomyces cerevisiae S288C

UniProt Q03761

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain I； UniProt 1–539 Not recorded Transcription factor SPT20 × 1 （P50875） Transcription-associated protein 1 × 1 （P38811） 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

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 6T9J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–539（539 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
6T9K SAGA Core module Deposited 2019-10-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 1–539（539 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 3.30 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TAF12_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I； PDBConstruct 1–539； UniProt 1–539

Transcription-associated protein 1

Saccharomyces cerevisiae S288C

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain T； UniProt 1–3744 Not recorded Transcription factor SPT20 × 1 （P50875） Transcription initiation factor TFIID subunit 12 × 1 （Q03761） 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

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 6T9J 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 oligomeric state 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
6IG9 Tra1 subunit from Saccharomyces cerevisiae SAGA complex Deposited 2018-09-25 Different oligomeric state 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 8.5；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
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different oligomeric state 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
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 3
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 6t9j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6t9j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6t9j
Deposition date deposition_date2019-10-28
Structure title titleSAGA Tra1 module
Keywords keywordsCoactivator, Transcription, Histone acetyltransferase, Histone deubiquitinase, GENE REGULATION; GENE REGULATION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier58.87 Å
Radius of gyration Rg (electron density) rg_electron58.78 Å
Forward intensity I(0) i02230060000.00
Molecular weight molecular_weight418980.0 kDa
Excluded volume excluded_volume533060 ų
Envelope volume envelope_volume793770 ų
Hydration-shell volume shell_volume110280 ų
Envelope diameter envelope_diameter197.5 Å
Shell Rg shell_rg63.80 Å
Envelope Rg envelope_rg57.31 Å
Shape Rg shape_rg58.78 Å
Total Rg total_rg58.89 Å
Total atoms total_atoms29550
Residues n_residues3617
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 dmax205.5 Å
Rg (real space) rg_real58.95 Å
Rg uncertainty (real space) rg_real_error2.17 Å
I(0) (real space) i0_real2.2300e+09
I(0) uncertainty (real space) i0_real_error4.1280e+07
Rg (reciprocal space) rg_reciprocal58.78 Å
I(0) (reciprocal space) i0_reciprocal2229000000.0000
Solution quality estimate total_estimate0.8695
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary60.9 Å
Skewness Skewness skewness0.339
Kurtosis Kurtosis kurtosis-0.464
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha193900000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.809
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)