SAXSdb — 5c6v

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

ASPR2 protein

Oryza sativa

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–209 Chain B； UniProt 1–209 Chain C； UniProt 1–209 Chain D； UniProt 1–209	Fragment：N-terminal domain (UNP residues 1-209)	AFP homolog 2 × 4 （Q9SV55）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% w/v PEG 3,350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5, 3.0% w/v D-(+)-glucose monohydrate	Resolution 3.10 Å R-free 0.286

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 5C6V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ZHE Crystal structure of the SeMet substituted Topless related protein 2 (TPR2) N-terminal domain (1-209) from rice Deposited 2015-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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 6.5；293 K；25% w/v PEG 3,350, 0.2 M Magnesium chloride, 0.1 M BIS-TRIS, pH 6.5, 19.6 mM 5-Methyl-6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside	Resolution 2.50 Å R-free 0.242
5C6Q Crystal structure of the apo TOPLESS related protein 2 (TPR2) N-terminal domain (1-209) from rice Deposited 2015-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2 M magnesium chloride, 0.1 M BIS-TRIS, pH 6.5	Resolution 3.25 Å R-free 0.270
5C7E Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA10 peptide Deposited 2015-06-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% w/v PEG 3,350, 0.2 M sodium citrate tribasic dihydrate	Resolution 3.10 Å R-free 0.229
5C7E Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA10 peptide Deposited 2015-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain F 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% w/v PEG 3,350, 0.2 M sodium citrate tribasic dihydrate	Resolution 3.10 Å R-free 0.229
5C7F Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA1 peptide Deposited 2015-06-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% w/v PEG 3,350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5	Resolution 2.70 Å R-free 0.256
5J9K Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) in complex with rice D53 repressor EAR peptide motif Deposited 2016-04-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% w/v Polyethylene glycol 3350, 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, pH 6.5	Resolution 2.55 Å R-free 0.253
5JA5 Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A and L130A mutant in complex with rice D53 repressor EAR peptide motif Deposited 2016-04-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；293 K；20% w/v Polyethylene glycol 3350, 0.2 M Potassium phosphate monobasic, pH 4.8	Resolution 2.00 Å R-free 0.228
5JGC Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A, L130A, L179A and I195A mutant Deposited 2016-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% w/v Polyethylene glycol 4000, 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5	Resolution 2.08 Å R-free 0.246
5JHP Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L179A and I195A mutant in complex with rice D53 repressor EAR peptide motif Deposited 2016-04-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；20% w/v Polyethylene glycol 3350, 0.2 M Lithium sulfate monohydrate, pH 6.0	Resolution 3.15 Å R-free 0.284

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5NBT9_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–209； UniProt 1–209 Author chain B； PDBConstruct 1–209； UniProt 1–209 Author chain C； PDBConstruct 1–209； UniProt 1–209 Author chain D； PDBConstruct 1–209； UniProt 1–209

AFP homolog 2

OrganismNot specified

UniProt Q9SV55

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain E； UniProt 4–14 Chain F； UniProt 4–14 Chain G； UniProt 4–14 Chain H； UniProt 4–14	Fragment：UNP residues 4-14	ASPR2 protein × 4 （Q5NBT9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% w/v PEG 3,350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5, 3.0% w/v D-(+)-glucose monohydrate	Resolution 3.10 Å R-free 0.286

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 5C6V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8T2I Negative stain EM assembly of MYC, JAZ, and NINJA complex Deposited 2023-06-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 1–425（425 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8	Resolution 10.40 Å

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

View Construct and Data Evidence

UniProt name	NINJA_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–11； UniProt 4–14 Author chain F； PDBConstruct 1–11； UniProt 4–14 Author chain G； PDBConstruct 1–11； UniProt 4–14 Author chain H； PDBConstruct 1–11； UniProt 4–14

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	5c6v
Deposition date deposition_date	2015-06-23
Structure title title	Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis NINJA peptide
Keywords keywords	;transcriptional corepressor, alpha-helical structure, tetrameric protein, plant transcriptional repression, TRANSCRIPTION, Plant development ;; 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	38.88 Å
Radius of gyration Rg (electron density) rg_electron	39.01 Å
Forward intensity I(0) i0	133225000.00
Molecular weight molecular_weight	97431.0 kDa
Excluded volume excluded_volume	123780 Å³
Envelope volume envelope_volume	166150 Å³
Hydration-shell volume shell_volume	37945 Å³
Envelope diameter envelope_diameter	154.5 Å
Shell Rg shell_rg	41.49 Å
Envelope Rg envelope_rg	38.73 Å
Shape Rg shape_rg	38.98 Å
Total Rg total_rg	39.27 Å
Total atoms total_atoms	6880
Residues n_residues	830
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	144.9 Å
Rg (real space) rg_real	39.44 Å
Rg uncertainty (real space) rg_real_error	1.75 Å
I(0) (real space) i0_real	1.3320e+08
I(0) uncertainty (real space) i0_real_error	2.3880e+06
Rg (reciprocal space) rg_reciprocal	39.09 Å
I(0) (reciprocal space) i0_reciprocal	133200000.0000
Solution quality estimate total_estimate	0.8037
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.9 Å
Skewness Skewness skewness	0.673
Kurtosis Kurtosis kurtosis	0.235
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10210000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.610; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.767; Smooth: 0.847

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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	ASPR2 protein
Molecular weight formula_weight	24903.6 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
Atom count atom_count	6914

MSSLSRELVFLILQFLDEEKFKETVHKLEQESGFFFNMKYFEEKVHAGEWDEVEKYLSGFTKVDDNRYSMKIFFEIRKQKYLEALDRHDRAKAVDILVKDLKVFSTFNEELYKEITQLLTLENFRENEQLSKYGDTKSARSIMLIELKKLIEANPLFREKLVFPTLKASRLRTLINQSLNWQHQLCKNPRPNPDIKTLFTDHTCTPPNG

来源 Source

来源生物 organism	Oryza sativa
通用名 common_name	Rice
NCBI Class编号 ncbi_taxonomy_id	4530
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	AFP homolog 2
Molecular weight formula_weight	1117.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

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

DNGLELSLGLS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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8. Citations (1)

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Unit-cell length a length_a	81.743 Å
Unit-cell length b length_b	65.042 Å
Unit-cell length c length_c	107.735 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	48.495 Å
R factor r_factor	0.2349
R_work r_work	0.2323
R_free r_free	0.2864

fit	/app/data/saxs_computation/c6/5c6v/5c6v.fit
pddf	/app/data/pr_computation/c6/5c6v/5c6v.pr.out
profile	/app/data/saxs_computation/c6/5c6v/5c6v.dat

Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis NINJA peptide

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

ASPR2 protein

State in the Current Structure

Other States of the Same Protein in the Database

AFP homolog 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 (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)