SAXSdb — 4ywc

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

Transcription factor MYC3

Arabidopsis thaliana

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 5–242	Fragment：N-terminal domain (UNP residues 5-242)	Protein TIFY 7 × 1 （Q8W4J8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；The purified proteins at a concentration of 15 mg/ml are mixed with 0.2 M magnesium nitrate, 20% (w/v) polyethylene glycol 3,350. Crystals of about 100 um in length appeared in 3 days	Resolution 2.40 Å R-free 0.295
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 5–242	Fragment：N-terminal domain (UNP residues 5-242)	Protein TIFY 7 × 1 （Q8W4J8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；The purified proteins at a concentration of 15 mg/ml are mixed with 0.2 M magnesium nitrate, 20% (w/v) polyethylene glycol 3,350. Crystals of about 100 um in length appeared in 3 days	Resolution 2.40 Å R-free 0.295

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 4YWC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4RQW Crystal structure of Myc3 N-terminal JAZ-binding domain [44-238] from Arabidopsis Deposited 2014-11-05	Different construct 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 44–238（195 aa） Fragment：Myc3 N-terminal JAZ-binding domain (UNP residues 44-238)	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% (w/v) polyethylene glycol 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.263
4RQW Crystal structure of Myc3 N-terminal JAZ-binding domain [44-238] from Arabidopsis Deposited 2014-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 44–238（195 aa） Fragment：Myc3 N-terminal JAZ-binding domain (UNP residues 44-238)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% (w/v) polyethylene glycol 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.263
4RQW Crystal structure of Myc3 N-terminal JAZ-binding domain [44-238] from Arabidopsis Deposited 2014-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 44–238（195 aa） Fragment：Myc3 N-terminal JAZ-binding domain (UNP residues 44-238) Chain B 44–238（195 aa） Fragment：Myc3 N-terminal JAZ-binding domain (UNP residues 44-238)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% (w/v) polyethylene glycol 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.263
4RRU Myc3 N-terminal JAZ-binding domain[5-242] from arabidopsis Deposited 2014-11-06	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 5–242（238 aa） Fragment：Myc3 N-terminal JAZ-binding domain (UNP residues 5-242)	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 30% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.276
4RRU Myc3 N-terminal JAZ-binding domain[5-242] from arabidopsis Deposited 2014-11-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 5–242（238 aa） Fragment：Myc3 N-terminal JAZ-binding domain (UNP residues 5-242)	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 30% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.276
4RS9 Structure of Myc3 N-terminal JAZ-binding domain [44-238] in complex with Jas motif of JAZ9 Deposited 2014-11-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 44–238（195 aa） Fragment：N-terminal JAZ-binding domain (UNP residues 44-238)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, and 30% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.95 Å R-free 0.234
4YZ6 Crystal Structure of Myc3[44-238] from Arabidopsis in complex with Jaz1 peptide [200-221] Deposited 2015-03-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 44–238（195 aa） Fragment：UNP residues 44-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；The MYC3(44-238)-JAZ1 complex crystals were grown at 20 degree in sitting drops containing 0.2 ul of the purified complex proteins at a concentration of 15 mg/ml and 0.2 ul of well solution containing 3.5 M sodium formate. Crystals of about 80 um in length appeared in 2 days	Resolution 1.95 Å R-free 0.217
5T0F Crystal structure of the Myc3 N-terminal domain [44-242] in complex with JAZ10 CMID domain [16-58] from arabidopsis Deposited 2016-08-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 44–242（199 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Tris, pH 6.0, 20% (w/v) polyethylene glycol monomethyl ether 2,000	Resolution 2.40 Å R-free 0.270
5T0Q Crystal structure of the Myc3 N-terminal domain [44-242] in complex with JAZ10 Jas domain [166-192] from arabidopsis Deposited 2016-08-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 44–242（199 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% w/v polyethylene glycol 3,350, 0.2 M magnesium formate dihydrate, pH 7.0.	Resolution 2.15 Å R-free 0.242
7FDM Crystal structure of transcription factor MYB29 in complex with MYC3 Deposited 2021-07-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 44–238（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES pH 7.0, 20% (w/v) PEG 6000, 0.2 M Sodium chloride	Resolution 2.50 Å R-free 0.268
7FDM Crystal structure of transcription factor MYB29 in complex with MYC3 Deposited 2021-07-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 44–238（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES pH 7.0, 20% (w/v) PEG 6000, 0.2 M Sodium chloride	Resolution 2.50 Å R-free 0.268
8T2I Negative stain EM assembly of MYC, JAZ, and NINJA complex Deposited 2023-06-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 49–238（190 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8	Resolution 10.40 Å

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MYC3_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–238； UniProt 5–242 Author chain B； PDBConstruct 1–238； UniProt 5–242

Protein TIFY 7

OrganismNot specified

UniProt Q8W4J8

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 C； UniProt 194–215	Fragment：UNP residues 194-215	Transcription factor MYC3 × 1 （Q9FIP9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；The purified proteins at a concentration of 15 mg/ml are mixed with 0.2 M magnesium nitrate, 20% (w/v) polyethylene glycol 3,350. Crystals of about 100 um in length appeared in 3 days	Resolution 2.40 Å R-free 0.295
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 194–215	Fragment：UNP residues 194-215	Transcription factor MYC3 × 1 （Q9FIP9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；The purified proteins at a concentration of 15 mg/ml are mixed with 0.2 M magnesium nitrate, 20% (w/v) polyethylene glycol 3,350. Crystals of about 100 um in length appeared in 3 days	Resolution 2.40 Å R-free 0.295

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 4YWC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4RS9 Structure of Myc3 N-terminal JAZ-binding domain [44-238] in complex with Jas motif of JAZ9 Deposited 2014-11-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 218–239（22 aa） Fragment：Jas motif (UNP residues 218-239)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, and 30% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.95 Å R-free 0.234

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

View Construct and Data Evidence

UniProt name	TIF7_ARATH
Isoform	Q8W4J8-2
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–22； UniProt 194–215 Author chain D； PDBConstruct 1–22； UniProt 194–215

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	4ywc
Deposition date deposition_date	2015-03-20
Structure title title	Crystal structure of Myc3(5-242) fragment in complex with Jaz9(218-239) peptide
Keywords keywords	helix-sheet-helix sandwich fold, Jasmonate signaling, Myc transcription factor, Myc-Jaz complex, TRANSCRIPTION REGULATOR; TRANSCRIPTION REGULATOR
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	23.82 Å
Radius of gyration Rg (electron density) rg_electron	22.68 Å
Forward intensity I(0) i0	34795100.00
Molecular weight molecular_weight	43809.0 kDa
Excluded volume excluded_volume	54153 Å³
Envelope volume envelope_volume	67699 Å³
Hydration-shell volume shell_volume	24973 Å³
Envelope diameter envelope_diameter	76.5 Å
Shell Rg shell_rg	29.51 Å
Envelope Rg envelope_rg	22.78 Å
Shape Rg shape_rg	22.65 Å
Total Rg total_rg	23.58 Å
Total atoms total_atoms	3086
Residues n_residues	402
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	74.4 Å
Rg (real space) rg_real	23.75 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.4800e+07
I(0) uncertainty (real space) i0_real_error	4.4910e+05
Rg (reciprocal space) rg_reciprocal	23.77 Å
I(0) (reciprocal space) i0_reciprocal	34800000.0000
Solution quality estimate total_estimate	0.9072
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.262
Kurtosis Kurtosis kurtosis	-0.453
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8585000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

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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 factor MYC3
Molecular weight formula_weight	25954.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3186

TSSINFLTSDDDASAAAMEAFIGTNHHSSLFPPPPQQPPQPQFNEDTLQQRLQALIESAGENWTYAIFWQISHDFDSSTGDNTVILGWGDGYYKGEEDKEKKKNNTNTAEQEHRKRVIRELNSLISGGIGVSDESNDEEVTDTEWFFLVSMTQSFVNGVGLPGESFLNSRVIWLSGSGALTGSGCERAGQGQIYGLKTMVCIATQNGVVELGSSEVISQSSDLMHKVNNLFNFNNGGG

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	Mouse-ear cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	Protein TIFY 7
Molecular weight formula_weight	2622.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

SVPQARKASLARFLEKRKERLM

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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8. Citations (1)

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Unit-cell length a length_a	59.105 Å
Unit-cell length b length_b	110.627 Å
Unit-cell length c length_c	161.846 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	49.621 Å
R factor r_factor	0.2417
R_work r_work	0.2390
R_free r_free	0.2951

fit	/app/data/saxs_computation/yw/4ywc/4ywc.fit
pddf	/app/data/pr_computation/yw/4ywc/4ywc.pr.out
profile	/app/data/saxs_computation/yw/4ywc/4ywc.dat

Crystal structure of Myc3(5-242) fragment in complex with Jaz9(218-239) peptide

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

Transcription factor MYC3

State in the Current Structure

Other States of the Same Protein in the Database

Protein TIFY 7

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)