SAXSdb — 9yzy

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

histone acetyltransferase

OrganismNot specified

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 N； UniProt 1–405	Not recorded	Transcriptional adapter 2 × 1 （G0S7B2） ctAda3 × 1 （G0SD59）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.40 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 9YZY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YNV Histone Acetyl Transferase (HAT) module of ctSAGA Deposited 2025-10-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 1–405（405 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9YNW Tra1, Core and minimal HAT modules of ctSAGA, composite. Deposited 2025-10-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain N 1–405（405 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	G0SCB2_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain N； PDBConstruct 1–405； UniProt 1–405

Transcriptional adapter 2

OrganismNot specified

UniProt G0S7B2

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 M； UniProt 1–519	Not recorded	histone acetyltransferase × 1 （G0SCB2） ctAda3 × 1 （G0SD59）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.40 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 9YZY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YNV Histone Acetyl Transferase (HAT) module of ctSAGA Deposited 2025-10-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 1–519（519 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9YNW Tra1, Core and minimal HAT modules of ctSAGA, composite. Deposited 2025-10-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain M 1–519（519 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	G0S7B2_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–519； UniProt 1–519

ctAda3

OrganismNot specified

UniProt G0SD59

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 O； UniProt 1–730	Not recorded	histone acetyltransferase × 1 （G0SCB2） Transcriptional adapter 2 × 1 （G0S7B2）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.40 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 9YZY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YNV Histone Acetyl Transferase (HAT) module of ctSAGA Deposited 2025-10-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain O 1–730（730 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9YNW Tra1, Core and minimal HAT modules of ctSAGA, composite. Deposited 2025-10-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain O 1–730（730 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	G0SD59_CHATD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain O； PDBConstruct 1–730； UniProt 1–730

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yzy
Deposition date deposition_date	2025-10-30
Structure title title	ctSAGA Focused on HAT Bromodomain region
Keywords keywords	ctSAGA complex, Histone Acetyl Transferase (HAT) Module, Tra1 module and Core module, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	38.55 Å
Radius of gyration Rg (electron density) rg_electron	38.42 Å
Forward intensity I(0) i0	172876000.00
Molecular weight molecular_weight	104260.0 kDa
Excluded volume excluded_volume	129920 Å³
Envelope volume envelope_volume	189550 Å³
Hydration-shell volume shell_volume	44149 Å³
Envelope diameter envelope_diameter	148.5 Å
Shell Rg shell_rg	41.02 Å
Envelope Rg envelope_rg	38.32 Å
Shape Rg shape_rg	38.42 Å
Total Rg total_rg	38.60 Å
Total atoms total_atoms	14542
Residues n_residues	903
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	140.9 Å
Rg (real space) rg_real	38.92 Å
Rg uncertainty (real space) rg_real_error	1.59 Å
I(0) (real space) i0_real	1.7290e+08
I(0) uncertainty (real space) i0_real_error	3.2150e+06
Rg (reciprocal space) rg_reciprocal	38.69 Å
I(0) (reciprocal space) i0_reciprocal	172800000.0000
Solution quality estimate total_estimate	0.8332
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.2 Å
Skewness Skewness skewness	0.555
Kurtosis Kurtosis kurtosis	-0.065
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27420000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.817; Smooth: 0.879

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	histone acetyltransferase
Molecular weight formula_weight	46983.7 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N
Atom count atom_count	14542

MTSENGKRKATEEPGSPSAAKRIKQEPSETDKDKKEENKDKKTVAKPPPIPYPEKPAVIEERNGEIEFRVVNNDGERESLIILTGLKCIFQKQLPKMPKDYIARLVYDRTHLSIAIVKKPLEVVGGITYRPFKNRKFAEIVFCAISSDQQVKGYGAHLMSHLKDYVKATTNIEHFLTYADNYAIGYFKKQGFTKEITLDKSVWMGYIKDYEGGTIMQCTMIPRIRYLEQGRMLLKQKECVQAKIRAFSKSHIVHPPPKQWRNGNVTPIDPLSIDAIRESGWSPDMDELARQPRHGPNYNQLLHLLNDMQNHASSWPFLVPVNKDEVVDYYDIIKEPMDLSTMESKLEADQYQTPEDFIRDAKLIFDNCRKYNNENTPYAKSANKLEKFMWQQIRQIPEWSHLEPS

Entity 2 Entity 2 polymer

Description description	Transcriptional adapter 2
Molecular weight formula_weight	58866.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MGVIRKKIAGRSGEGGVKYICDVCSVDITSTVRIRCADPACHDYDLCVPCFANGSSSNAHKPATHSFRVIEQNSFPIFDPDWGADEELLLLEGAEIYGLGSWADIADHIGGYRTKDEVRDHYLKVYIESPNFPLPERCSPYDLELPNSISREEFQARKKRRIEERREAAKNAPPPQPKTKPTASIPACHEIQGYMPGRLEFETEYCNEAEEAVQLMSFDPGDGINPRTGELEPEMELKLTVMEIYNNRLTQRVERKKVIFEHNLLEYRENTKAEKKRSREERELLNKAKPFARMMNRHDFEQFCQGLIDELNLRQAIAQLQEWRSMRIGDLKSGEKYEQEKALRIQKSMPMGSLDRERLATSQRGKNQQQPEPPSGAALLVAPELPARYKEPIIDANGFPRPDANRLTVDGGSVVVANGTSQPKPKYVPPPVPGVQPMNLTQDNAPDLHLLTPEEIKLCETLRIQPKPYIMIKEQILKEAVKGNGSLKKKQAKEICRLDSQKGGRIFDFMVNAGWVVKA

Entity 3 Entity 3 polymer

Description description	ctAda3
Molecular weight formula_weight	79972.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MAPSSSQKGTGKKAGSAASAIRSHQQHSQQQRSRNTTPGPAGIPPTSSTSVSVSVASLPPIETVETETLDLRFDTFRNVTFEDLVDPAAASALIPDSKSLDGIISRLQRLADIIEKRGANCDRGMRLLAQTRRQRLDELAVERGREEERRQAEADDEKKANKKKRKADSLAPGAVNTERSSPNRESTSKARKLDRDDTASSSLSPAAAGTPSNMDVDDKDKEKDKDKTKAEADSDSDSDDGAPPPPPRPPANVFGDDPSTFPDPTVYEIRPVLPGMSEEEIKEIYSVASYPKSDLAHLTCGEPPDRDFSNSKPTNQINFSTFSSYIEPYFRPFTEEDLAFLRERGDRVTPFIMPKRGKKHYTEIWAEEDGAMAIDSSPPGGRDRLPPNQARGSIDNMDDEVAETDKLSVGPLLTRLLQAMRPENRAPTADDKSGPNGTSGDGDGPQQSFDFNDSTAAPNPSQSQPNGVNGVAATTNGDSQQQQQQQQHQSLPPATFMPESNTEAWKKATHPKLDYNQVDERIKQELRHIGFLPLPPSSATDPSNSSASVTPAAPPPPGTTATTAEYDGHYDDEVAARLRVLQARLREQILLNGARKARLTELVKERMAYQEYQTILEDLDAQVNAAYLKRTRTMGKKPKKNRPGQHSSGSAAAAAAAAAGMARPGIGDLARTLMDRRRRWIEQIGAVFDDEGITKCPRVEDGDTSIFGREIMAELIKREKEAWDEEVEEE

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	4.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	384825

fit	/app/data/saxs_computation/yz/9yzy/9yzy.fit
pddf	/app/data/pr_computation/yz/9yzy/9yzy.pr.out
profile	/app/data/saxs_computation/yz/9yzy/9yzy.dat

ctSAGA Focused on HAT Bromodomain region

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

histone acetyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional adapter 2

State in the Current Structure

Other States of the Same Protein in the Database

ctAda3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)