SAXSdb — 1egw

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

MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A

Homo sapiens

UniProt Q02078

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 Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 2–78 Chain B； UniProt 2–78	Fragment：N-TERMINUS, RESIDUES 2-78	;DNA (5'-D(APAPAPGPCPTPAPTPTPAPTPTPAPGPCPTPT)-3') ; × 1 ;DNA (5'-D(TPAPAPGPCPTPAPAPTPAPAPTPAPGPCPTPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；PEG 6000, NaCl, Ba(NO3)2, sodium Acetate, Bis-tris buffer, DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.229
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 2–78 Chain D； UniProt 2–78	Fragment：N-TERMINUS, RESIDUES 2-78	;DNA (5'-D(APAPAPGPCPTPAPTPTPAPTPTPAPGPCPTPT)-3') ; × 1 ;DNA (5'-D(TPAPAPGPCPTPAPAPTPAPAPTPAPGPCPTPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；PEG 6000, NaCl, Ba(NO3)2, sodium Acetate, Bis-tris buffer, DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.229

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 1EGW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C7U Complex of the DNA binding core domain of the transcription factor MEF2A with a 20mer oligonucleotide Deposited 2000-03-17	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–86（85 aa） Fragment：RESIDUES 2-86 Chain B 2–86（85 aa） Fragment：RESIDUES 2-86	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；308 K	Resolution not provided
1LEW CRYSTAL STRUCTURE OF MAP KINASE P38 COMPLEXED TO THE DOCKING SITE ON ITS NUCLEAR SUBSTRATE MEF2A Deposited 2002-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 269–280（12 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；PEG 8000, HEPES, pH 7.5, VAPOR DIFFUSION, temperature 289K	Resolution 2.30 Å R-free 0.257
3KOV Structure of MEF2A bound to DNA reveals a completely folded MADS-box/MEF2 domain that recognizes DNA and recruits transcription co-factors Deposited 2009-11-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	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 hanging drop；pH 4.7；291 K；50 mM acetic acid, 142mM NaCl, 5mM MgCl2, 10mM CaCl2, 3.3% Glycerol, 22.5% 3K PEG, pH 4.7, hanging drop, temperature 291K	Resolution 2.90 Å R-free 0.279
3KOV Structure of MEF2A bound to DNA reveals a completely folded MADS-box/MEF2 domain that recognizes DNA and recruits transcription co-factors Deposited 2009-11-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain I 2–91（90 aa） Chain J 2–91（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 4.7；291 K；50 mM acetic acid, 142mM NaCl, 5mM MgCl2, 10mM CaCl2, 3.3% Glycerol, 22.5% 3K PEG, pH 4.7, hanging drop, temperature 291K	Resolution 2.90 Å R-free 0.279
3MU6 Inhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by Small Molecules Deposited 2010-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–72（71 aa） Chain B 2–72（71 aa）	Mutation：E71A Mutation：E71A	BXL (3E)-N~8~-(2-aminophenyl)-N~1~-phenyloct-3-enediamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 4.7；291 K；50 mM acetic acid, 142mM NaCl, 5mM MgCl2, 10mM CaCl2, 3.3% Glycerol, 22.5% 3K PEG, pH 4.7, hanging drop, temperature 291K	Resolution 2.43 Å R-free 0.251
3MU6 Inhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by Small Molecules Deposited 2010-05-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 2–72（71 aa） Chain D 2–72（71 aa）	Mutation：E71A Mutation：E71A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 4.7；291 K；50 mM acetic acid, 142mM NaCl, 5mM MgCl2, 10mM CaCl2, 3.3% Glycerol, 22.5% 3K PEG, pH 4.7, hanging drop, temperature 291K	Resolution 2.43 Å R-free 0.251
3P57 Crystal structure of the p300 TAZ2 domain bound to MEF2 on DNA Deposited 2010-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: tridecameric	Chain A 2–91（90 aa） Fragment：N terminal domain (UNP residues 2-91) Chain B 2–91（90 aa） Fragment：N terminal domain (UNP residues 2-91) Chain C 2–91（90 aa） Fragment：N terminal domain (UNP residues 2-91) Chain D 2–91（90 aa） Fragment：N terminal domain (UNP residues 2-91) Chain I 2–91（90 aa） Fragment：N terminal domain (UNP residues 2-91) Chain J 2–91（90 aa） Fragment：N terminal domain (UNP residues 2-91)	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；288 K；16% PEG 1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.19 Å R-free 0.272
6BYY MEF2 CHIMERA/DNA Complex Deposited 2017-12-21	Different construct Different mutation/modification 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 1–64（64 aa） Chain A 92–95（4 aa） Chain B 1–64（64 aa） Chain B 92–95（4 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 mutation/modification 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 1–64（64 aa） Chain C 92–95（4 aa） Chain D 1–64（64 aa） Chain D 92–95（4 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 1–64（64 aa） Chain C 92–95（4 aa） Chain D 1–64（64 aa） Chain D 92–95（4 aa）	Mutation：D83V Mutation：D83V 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 1–64（64 aa） Chain A 92–95（4 aa） Chain B 1–64（64 aa） Chain B 92–95（4 aa）	Mutation：D83V Mutation：D83V 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
6WC2 Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex Deposited 2020-03-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 1–72（72 aa） Chain A 92–95（4 aa） Chain B 1–72（72 aa） Chain B 92–95（4 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–72（72 aa） Chain C 92–95（4 aa） Chain D 1–72（72 aa） Chain D 92–95（4 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric	Chain I 1–72（72 aa） Chain I 92–95（4 aa） Chain J 1–72（72 aa） Chain J 92–95（4 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

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MEF2A_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–77； UniProt 2–78 Author chain B； PDBConstruct 1–77； UniProt 2–78 Author chain C； PDBConstruct 1–77； UniProt 2–78 Author chain D； PDBConstruct 1–77； UniProt 2–78

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	1egw
Deposition date deposition_date	2000-02-17
Structure title title	CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA
Keywords keywords	MADS-box transcription factor, DNA-protein complex, transcription/DNA, TRANSCRIPTION-DNA complex; TRANSCRIPTION/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	28.06 Å
Radius of gyration Rg (electron density) rg_electron	27.26 Å
Forward intensity I(0) i0	70050300.00
Molecular weight molecular_weight	53671.0 kDa
Excluded volume excluded_volume	61997 Å³
Envelope volume envelope_volume	82547 Å³
Hydration-shell volume shell_volume	25960 Å³
Envelope diameter envelope_diameter	95.3 Å
Shell Rg shell_rg	33.49 Å
Envelope Rg envelope_rg	27.03 Å
Shape Rg shape_rg	27.25 Å
Total Rg total_rg	27.84 Å
Total atoms total_atoms	3682
Residues n_residues	354
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	89.2 Å
Rg (real space) rg_real	28.13 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	7.0050e+07
I(0) uncertainty (real space) i0_real_error	1.0340e+06
Rg (reciprocal space) rg_reciprocal	28.11 Å
I(0) (reciprocal space) i0_reciprocal	70050000.0000
Solution quality estimate total_estimate	0.9007
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.3 Å
Skewness Skewness skewness	0.332
Kurtosis Kurtosis kurtosis	-0.505
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2928000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.900

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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	;DNA (5'-D(APAPAPGPCPTPAPTPTPAPTPTPAPGPCPTP*T)-3') ;
Molecular weight formula_weight	5200.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,H
Atom count atom_count	5926

AAAGCTATTATTAGCTT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPAPAPGPCPTPAPAPTPAPAPTPAPGPCPTP*T)-3') ;
Molecular weight formula_weight	5209.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,G

TAAGCTAATAATAGCTT

Entity 3 Entity 3 polymer

Description description	MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
Molecular weight formula_weight	9155.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEYNEPHES

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	656

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1egwa_
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	d1egwb_
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	d1egwc_
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	d1egwd_
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	1egwA01
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	1egwB01
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	1egwC01
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	1egwD01
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	41.371 Å
Unit-cell length b length_b	60.696 Å
Unit-cell length c length_c	63.987 Å
Unit-cell angle α angle_alpha	115.18 °
Unit-cell angle β angle_beta	89.99 °
Unit-cell angle γ angle_gamma	90.00 °
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	1.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2060
R_free r_free	0.2290

fit	/app/data/saxs_computation/eg/1egw/1egw.fit
pddf	/app/data/pr_computation/eg/1egw/1egw.pr.out
profile	/app/data/saxs_computation/eg/1egw/1egw.dat

CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA

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

MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A

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 water

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)