SAXSdb — 1tqe

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

Myocyte-specific enhancer factor 2B

Homo sapiens

UniProt Q02080

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–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain P； UniProt 1–93 Chain Q； UniProt 1–93	Fragment：residues 1-93	MEF2 binding site of nur77 promoter × 1 MEF2 binding site of nur77 promoter × 1 Histone deacetylase 9 × 1 （Q99N13）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.35；315 K；BTP, PEG, NaCl, glycerol, MgCl2, CaCl2, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 315K	Resolution 2.70 Å R-free 0.289
2	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain R； UniProt 1–93 Chain S； UniProt 1–93	Fragment：residues 1-93	MEF2 binding site of nur77 promoter × 1 MEF2 binding site of nur77 promoter × 1 Histone deacetylase 9 × 1 （Q99N13）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.35；315 K；BTP, PEG, NaCl, glycerol, MgCl2, CaCl2, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 315K	Resolution 2.70 Å R-free 0.289

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 1TQE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N6J Structural basis of sequence-specific recruitment of histone deacetylases by Myocyte Enhancer Factor-2 Deposited 2002-11-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 2–94（93 aa） Fragment：residues 2-91, MADS-box/MEF2S domain Chain B 2–94（93 aa） Fragment：residues 2-91, MADS-box/MEF2S domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 3500, sodium cholride, BTP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.268
6BYY MEF2 CHIMERA/DNA Complex Deposited 2017-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 65–91（27 aa） Chain B 65–91（27 aa）	Not recorded	1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M HAc pH 4.7, 150 mM NaCl, 10 mM CaCl2, 5 mM MgCl2 and 28% PEG 400	Resolution 2.30 Å R-free 0.266
6BYY MEF2 CHIMERA/DNA Complex Deposited 2017-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 65–91（27 aa） Chain D 65–91（27 aa）	Not recorded	TCE 3,3',3''-phosphanetriyltripropanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M HAc pH 4.7, 150 mM NaCl, 10 mM CaCl2, 5 mM MgCl2 and 28% PEG 400	Resolution 2.30 Å R-free 0.266
6BZ1 MEF2 Chimera D83V mutant/DNA complex Deposited 2017-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 65–91（27 aa） Chain D 65–91（27 aa）	Mutation：D83V Mutation：D83V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1M MES pH 5.94, 0.2 M NaCl and 18% PEG2000MME	Resolution 2.97 Å R-free 0.190
6BZ1 MEF2 Chimera D83V mutant/DNA complex Deposited 2017-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 65–91（27 aa） Chain B 65–91（27 aa）	Mutation：D83V Mutation：D83V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1M MES pH 5.94, 0.2 M NaCl and 18% PEG2000MME	Resolution 2.97 Å R-free 0.190
6C9L MEF2B Apo Protein Structure Deposited 2018-01-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–93（93 aa） Chain B 1–93（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M NaCl, 0.1 M Bis-Tris pH 5.5, 20% PEG3350	Resolution 2.30 Å R-free 0.235
6C9L MEF2B Apo Protein Structure Deposited 2018-01-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–93（93 aa） Chain D 1–93（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M NaCl, 0.1 M Bis-Tris pH 5.5, 20% PEG3350	Resolution 2.30 Å R-free 0.235
6C9L MEF2B Apo Protein Structure Deposited 2018-01-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–93（93 aa） Chain F 1–93（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M NaCl, 0.1 M Bis-Tris pH 5.5, 20% PEG3350	Resolution 2.30 Å R-free 0.235
6WC2 Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex Deposited 2020-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 73–91（19 aa） Chain B 73–91（19 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.15 M DL-Malic acid pH 7.0, 20% Polyethylene glycol 3350	Resolution 2.10 Å R-free 0.225
6WC2 Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex Deposited 2020-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 73–91（19 aa） Chain D 73–91（19 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.15 M DL-Malic acid pH 7.0, 20% Polyethylene glycol 3350	Resolution 2.10 Å R-free 0.225
6WC2 Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex Deposited 2020-03-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric	Chain I 73–91（19 aa） Chain J 73–91（19 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.15 M DL-Malic acid pH 7.0, 20% Polyethylene glycol 3350	Resolution 2.10 Å R-free 0.225
6WC5 Crystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DNA Complex Deposited 2020-03-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 2–91（90 aa） Chain B 2–91（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM HEPES pH 7.0, 18% PEG 2000	Resolution 2.90 Å R-free 0.251
6WC5 Crystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DNA Complex Deposited 2020-03-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 2–91（90 aa） Chain D 2–91（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM HEPES pH 7.0, 18% PEG 2000	Resolution 2.90 Å R-free 0.251

6 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MEF2B_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–93； UniProt 1–93 Author chain Q； PDBConstruct 1–93； UniProt 1–93 Author chain R； PDBConstruct 1–93； UniProt 1–93 Author chain S； PDBConstruct 1–93； UniProt 1–93

Histone deacetylase 9

Mus musculus

UniProt Q99N13

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–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain X； UniProt 138–158	Fragment：residues 138-158	MEF2 binding site of nur77 promoter × 1 MEF2 binding site of nur77 promoter × 1 Myocyte-specific enhancer factor 2B × 2 （Q02080）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.35；315 K；BTP, PEG, NaCl, glycerol, MgCl2, CaCl2, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 315K	Resolution 2.70 Å R-free 0.289
2	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain Y； UniProt 138–158	Fragment：residues 138-158	MEF2 binding site of nur77 promoter × 1 MEF2 binding site of nur77 promoter × 1 Myocyte-specific enhancer factor 2B × 2 （Q02080）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.35；315 K；BTP, PEG, NaCl, glycerol, MgCl2, CaCl2, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 315K	Resolution 2.70 Å R-free 0.289

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	HDAC9_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain X； PDBConstruct 6–26； UniProt 138–158 Author chain Y； PDBConstruct 6–26； UniProt 138–158

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	1tqe
Deposition date deposition_date	2004-06-17
Structure title title	Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2
Keywords keywords	MEF2, HDAC, co-repressor, transcription, TRANSCRIPTION-PROTEIN BINDING-DNA COMPLEX; TRANSCRIPTION/PROTEIN BINDING/DNA
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	31.07 Å
Radius of gyration Rg (electron density) rg_electron	29.50 Å
Forward intensity I(0) i0	105943000.00
Molecular weight molecular_weight	68544.0 kDa
Excluded volume excluded_volume	80411 Å³
Envelope volume envelope_volume	107450 Å³
Hydration-shell volume shell_volume	31272 Å³
Envelope diameter envelope_diameter	108.0 Å
Shell Rg shell_rg	35.74 Å
Envelope Rg envelope_rg	29.07 Å
Shape Rg shape_rg	29.40 Å
Total Rg total_rg	30.26 Å
Total atoms total_atoms	4730
Residues n_residues	474
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	103.2 Å
Rg (real space) rg_real	31.19 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.0590e+08
I(0) uncertainty (real space) i0_real_error	1.5890e+06
Rg (reciprocal space) rg_reciprocal	31.14 Å
I(0) (reciprocal space) i0_reciprocal	105900000.0000
Solution quality estimate total_estimate	0.8730
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.4 Å
Skewness Skewness skewness	0.375
Kurtosis Kurtosis kurtosis	-0.486
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	9309000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.821

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	MEF2 binding site of nur77 promoter
Molecular weight formula_weight	5218.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E
Atom count atom_count	4730

AAAGCTATTTATAAGCA

Entity 2 Entity 2 polymer

Description description	MEF2 binding site of nur77 promoter
Molecular weight formula_weight	5191.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

TTGCTTATAAATAGCTT

Entity 3 Entity 3 polymer

Description description	Myocyte-specific enhancer factor 2B
Molecular weight formula_weight	11038.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R,S

MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRRGI

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 4 Entity 4 polymer

Description description	Histone deacetylase 9
Molecular weight formula_weight	2769.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y

SPKGTGASTEVKQKLQEFLLSKSATK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1tqep_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

Domain ID domain_id	d1tqeq_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

Domain ID domain_id	d1tqer_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

Domain ID domain_id	d1tqes_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

CATH v4.4 (4 domains)

Domain ID domain_id	1tqeP01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

Domain ID domain_id	1tqeQ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

Domain ID domain_id	1tqeR01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

Domain ID domain_id	1tqeS01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

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8. Citations (1)

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Unit-cell length a length_a	44.797 Å
Unit-cell length b length_b	66.930 Å
Unit-cell length c length_c	66.967 Å
Unit-cell angle α angle_alpha	76.67 °
Unit-cell angle β angle_beta	71.83 °
Unit-cell angle γ angle_gamma	71.81 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2630
R_free r_free	0.2890

fit	/app/data/saxs_computation/tq/1tqe/1tqe.fit
pddf	/app/data/pr_computation/tq/1tqe/1tqe.pr.out
profile	/app/data/saxs_computation/tq/1tqe/1tqe.dat

Mechanism of recruitment of class II histone deacetylases by myocyte enhancer factor-2

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

Myocyte-specific enhancer factor 2B

State in the Current Structure

Other States of the Same Protein in the Database

Histone deacetylase 9

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)