SAXSdb — 6cw3

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

Histone acetyltransferase GCN5

Saccharomyces cerevisiae S288c

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain H； UniProt 67–317	Not recorded	antibody heavy chain × 1 antibody light chain × 1 Transcriptional adapter 2 × 1 （Q02336） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；294 K；100 mM succinic acid pH 7.0, 15% w/v PEG3350	Resolution 1.98 Å R-free 0.227
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 67–317	Not recorded	antibody heavy chain × 1 antibody light chain × 1 Transcriptional adapter 2 × 1 （Q02336） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；294 K；100 mM succinic acid pH 7.0, 15% w/v PEG3350	Resolution 1.98 Å R-free 0.227

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 6CW3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E6I Bromodomain from GCN5 complexed with acetylated H4 peptide Deposited 2000-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 319–439（121 aa） Fragment：BROMODOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2.2M AMMONIUM SULPHATE, 20% V/V GLYCEROL, 4MM DITHIOTHREITOL, 100 MM HEPES PH 7.5, 125MM NACL 5:1 PEPTIDE:PROTEIN	Resolution 1.87 Å R-free 0.209
1YGH HAT DOMAIN OF GCN5 FROM SACCHAROMYCES CEREVISIAE Deposited 1999-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 99–262（164 aa） Fragment：HISTONE ACETYLTRANSFERASE DOMAIN	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；400 MM AMMONIUM SULFATE, 20% - 25% PEG 8000, pH 6.0	Resolution 1.90 Å R-free 0.236
1YGH HAT DOMAIN OF GCN5 FROM SACCHAROMYCES CEREVISIAE Deposited 1999-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 99–262（164 aa） Fragment：HISTONE ACETYLTRANSFERASE DOMAIN	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；400 MM AMMONIUM SULFATE, 20% - 25% PEG 8000, pH 6.0	Resolution 1.90 Å R-free 0.236
6CW2 Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 1 Deposited 2018-03-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 67–317（251 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.5；294 K；10 mM Tris-Cl pH 8.5, 200 mM Li2SO4, 25% w/v PEG3350	Resolution 2.67 Å R-free 0.284
6CW2 Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 1 Deposited 2018-03-29	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 67–317（251 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.5；294 K；10 mM Tris-Cl pH 8.5, 200 mM Li2SO4, 25% w/v PEG3350	Resolution 2.67 Å R-free 0.284

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCN5_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 4–254； UniProt 67–317 Author chain H； PDBConstruct 4–254； UniProt 67–317

Transcriptional adapter 2

Saccharomyces cerevisiae S288c

UniProt Q02336

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain G； UniProt 1–120	Not recorded	antibody heavy chain × 1 antibody light chain × 1 Histone acetyltransferase GCN5 × 1 （Q03330） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；294 K；100 mM succinic acid pH 7.0, 15% w/v PEG3350	Resolution 1.98 Å R-free 0.227
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–120	Not recorded	antibody heavy chain × 1 antibody light chain × 1 Histone acetyltransferase GCN5 × 1 （Q03330） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；294 K；100 mM succinic acid pH 7.0, 15% w/v PEG3350	Resolution 1.98 Å R-free 0.227

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 6CW3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ELJ Solution structure of the SWIRM domain of baker's yeast Transcriptional adapter 2 Deposited 2007-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 354–434（81 aa） Fragment：SWIRM	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.3mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADA2_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–120； UniProt 1–120 Author chain G； PDBConstruct 1–120； UniProt 1–120

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	6cw3
Deposition date deposition_date	2018-03-29
Structure title title	Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2
Keywords keywords	Ada2/Gcn5 structure, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	43.32 Å
Radius of gyration Rg (electron density) rg_electron	43.75 Å
Forward intensity I(0) i0	385246000.00
Molecular weight molecular_weight	158840.0 kDa
Excluded volume excluded_volume	198350 Å³
Envelope volume envelope_volume	272650 Å³
Hydration-shell volume shell_volume	57914 Å³
Envelope diameter envelope_diameter	206.1 Å
Shell Rg shell_rg	43.40 Å
Envelope Rg envelope_rg	44.09 Å
Shape Rg shape_rg	43.64 Å
Total Rg total_rg	44.09 Å
Total atoms total_atoms	11175
Residues n_residues	1470
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	118.1 Å
Rg (real space) rg_real	40.32 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	3.6660e+08
I(0) uncertainty (real space) i0_real_error	5.3760e+06
Rg (reciprocal space) rg_reciprocal	43.32 Å
I(0) (reciprocal space) i0_reciprocal	384900000.0000
Solution quality estimate total_estimate	0.6782
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.9 Å
Skewness Skewness skewness	0.446
Kurtosis Kurtosis kurtosis	-0.253
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.9912
Highest regularization parameter α highest_alpha	28080000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.010; Oscil: 0.961; Stabil: 0.978; 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 (6)

Entity 1 Entity 1 polymer

Description description	antibody heavy chain
Molecular weight formula_weight	25089.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	11837

EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSSYIHWVRQAPGKGLEWVASIYSYYGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWWQGMYEMGYGMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	antibody light chain
Molecular weight formula_weight	23338.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQGWANLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone acetyltransferase GCN5
Molecular weight formula_weight	29357.2 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H

MGSVTDVEKGIVKFEFDGVEYTFKERPSVVEENEGKIEFRVVNNDNTKENMMVLTGLKNIFQKQLPKMPKEYIARLVYDRSHLSMAVIRKPLTVVGGITYRPFDKREFAEIVFCAISSTEQVRGYGAHLMNHLKDYVRNTSNIKYFLTYADNYAIGYFKKQGFTKEITLDKSIWMGYIKDYEGGTLMQCSMLPRIRYLDAGKILLLQEAALRRKIRTISKSHIVRPGLEQFKDLNNIKPIDPMTIPGLKEAGWT

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Transcriptional adapter 2
Molecular weight formula_weight	13858.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G

GSNKFHCDVCSADCTNRVRVSCAICPEYDLCVPCFSQGSYTGKHRPYHDYRIIETNSYPILCPDWGADEELQLIKGAQTLGLGNWQDIADHIGSRGKEEVKEHYLKYYLESKYYPIPDITAG

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	662

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6cw3a_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6cw3b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6cw3b2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6cw3c_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6cw3d1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6cw3d2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	6cw3A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6cw3B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6cw3B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6cw3C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6cw3D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6cw3D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	101.657 Å
Unit-cell length b length_b	104.061 Å
Unit-cell length c length_c	166.335 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	88.219 Å
R factor r_factor	0.2037
R_work r_work	0.2025
R_free r_free	0.2273

fit	/app/data/saxs_computation/cw/6cw3/6cw3.fit
pddf	/app/data/pr_computation/cw/6cw3/6cw3.pr.out
profile	/app/data/saxs_computation/cw/6cw3/6cw3.dat

Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2

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

Histone acetyltransferase GCN5

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

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)