SAXSdb — 6miq

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

Transcription initiation factor TFIID subunit 14

Saccharomyces cerevisiae (strain ATCC 204508 / 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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–137	Fragment：YEATS domain residues 1-137	Histone H3K9bu × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；44% PEG600 (v/v) and 0.2 M citric acid (pH 6.0)	Resolution 1.75 Å R-free 0.218

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 6MIQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L7E The structure of a domain from yeast Deposited 2010-12-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–123（123 aa） Fragment：YEATS domain residues 1-123	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 0.12；Pressure ambient NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided
3QRL Crystal Structure of the Taf14 YEATS domain Deposited 2011-02-18	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 1–137（137 aa） Fragment：YEATS Domain (UNP Residues 1-137)	Not recorded	PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；42.5% (v/v) PEG-600, 100 mM Sodium Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.70 Å R-free 0.235
5D7E Crystal structure of Taf14 YEATS domain in complex with H3K9ac Deposited 2015-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–137（137 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M sodium citrate and 48% PEG600 (v/v)	Resolution 1.90 Å R-free 0.218
5IOK Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr Deposited 2016-03-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–137（137 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；44% PEG600 (v/v) and 0.2 M citric acid (pH 6.0)	Resolution 2.22 Å R-free 0.239
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric	Chain n 1–244（244 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 15.30 Å
6LQZ Solution structure of Taf14ET-Sth1EBMC Deposited 2020-01-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 174–244（71 aa） Fragment：Taf14ET	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Taf14ET, 1.5 mM [U-100% 13C; U-100% 15N] Sth1EBMC, 20 mM Phosphate buffer, 100 mM sodium chloride, 1 % v/v inhabitor cocktail, 0.04 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6MIN Crystal structure of Taf14 YEATS domain G82A mutant in complex with histone H3K9cr Deposited 2018-09-19	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–137（137 aa） Fragment：YEATS domain residues 1-137	Mutation：G82A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；44% PEG600 (v/v) and 0.2 M citric acid (pH 6.0)	Resolution 1.90 Å R-free 0.256
6MIO Crystal structure of Taf14 YEATS domain in complex with histone H3K9pr Deposited 2018-09-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–137（137 aa） Fragment：YEATS domain residues 1-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；46% PEG600 (v/v) and 0.2 M citric acid (pH 6.0)	Resolution 1.85 Å R-free 0.232
6MIP Crystal structure of Taf14 YEATS domain G82A mutant Deposited 2018-09-19	Different mutation/modification 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 1–137（137 aa） Fragment：YEATS domain residues 1-137	Mutation：G82A	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；48% PEG600 with 0.2 M sodium citrate (pH 6.0)	Resolution 2.00 Å R-free 0.219
7F4A Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide Deposited 2021-06-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–137（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；48% PEG 600, 0.04M citric acid	Resolution 2.00 Å R-free 0.204
7UHE Taf14 ET domain in complex with C-terminal tail of Taf2 Deposited 2022-03-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 168–243（76 aa） Fragment：ET domain Chain C 168–243（76 aa） Fragment：ET domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；2.4 M sodium malonate	Resolution 1.66 Å R-free 0.234
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 176–243（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 176–243（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 176–243（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 176–243（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
9UUO The NuA3 histone acetyltransferase complex Deposited 2025-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–244（244 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
9UUS The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail Deposited 2025-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–244（244 aa）	Not recorded	ZN ZINC ION × 5 ACO ACETYL COENZYME *A × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9VKW Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A Deposited 2025-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–244（244 aa）	Not recorded	ZN ZINC ION × 4 ACO ACETYL COENZYME *A × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å

15 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TAF14_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–142； UniProt 1–137

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	6miq
Deposition date deposition_date	2018-09-19
Structure title title	Crystal structure of Taf14 YEATS domain in complex with histone H3K9bu
Keywords keywords	Transcription, Epigenetic, Histone reader; TRANSCRIPTION
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	17.64 Å
Radius of gyration Rg (electron density) rg_electron	16.85 Å
Forward intensity I(0) i0	4862700.00
Molecular weight molecular_weight	16799.0 kDa
Excluded volume excluded_volume	21390 Å³
Envelope volume envelope_volume	24571 Å³
Hydration-shell volume shell_volume	13081 Å³
Envelope diameter envelope_diameter	61.1 Å
Shell Rg shell_rg	21.79 Å
Envelope Rg envelope_rg	17.34 Å
Shape Rg shape_rg	16.81 Å
Total Rg total_rg	17.86 Å
Total atoms total_atoms	1190
Residues n_residues	145
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	62.0 Å
Rg (real space) rg_real	17.71 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	4.8630e+06
I(0) uncertainty (real space) i0_real_error	6.5100e+04
Rg (reciprocal space) rg_reciprocal	17.71 Å
I(0) (reciprocal space) i0_reciprocal	4863000.0000
Solution quality estimate total_estimate	0.8380
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.0 Å
Skewness Skewness skewness	0.494
Kurtosis Kurtosis kurtosis	-0.115
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1135000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.680; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.986

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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	Transcription initiation factor TFIID subunit 14
Molecular weight formula_weight	16180.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1421

GPLGSMVATVKRTIRIKTQQHILPEVPPVENFPVRQWSIEIVLLDDEGKEIPATIFDKVIYHLHPTFANPNRTFTDPPFRIEEQGWGGFPLDISVFLLEKAGERKIPHDLNFLQESYEVEHVIQIPLNKPLLTEELAKSGST

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / 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

Entity 2 Entity 2 polymer

Description description	Histone H3K9bu
Molecular weight formula_weight	888.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

XQTARXST

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6miqA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1970 — YEATS domain

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8. Citations (1)

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Unit-cell length a length_a	113.149 Å
Unit-cell length b length_b	113.149 Å
Unit-cell length c length_c	26.170 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	56.575 Å
R factor r_factor	0.1745
R_work r_work	0.1719
R_free r_free	0.2178

fit	/app/data/saxs_computation/mi/6miq/6miq.fit
pddf	/app/data/pr_computation/mi/6miq/6miq.pr.out
profile	/app/data/saxs_computation/mi/6miq/6miq.dat

Crystal structure of Taf14 YEATS domain in complex with histone H3K9bu

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

Transcription initiation factor TFIID subunit 14

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)