SAXSdb — 6jrp

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

Protein capicua homolog

Homo sapiens

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 199–276	Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(APTPGPAPAPTPGPAPAPAPA)-3') ; × 1 ;DNA (5'-D(TPTPTPTPCPAPTPTPCPAPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain D； UniProt 199–276	Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(APTPGPAPAPTPGPAPAPAPA)-3') ; × 1 ;DNA (5'-D(TPTPTPTPCPAPTPTPCPAPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334
3	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain G； UniProt 199–276	Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(APTPGPAPAPTPGPAPAPAPA)-3') ; × 1 ;DNA (5'-D(TPTPTPTPCPAPTPTPCPAPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334
4	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain J； UniProt 199–276	Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(APTPGPAPAPTPGPAPAPAPA)-3') ; × 1 ;DNA (5'-D(TPTPTPTPCPAPTPTPCPAPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334

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 6JRP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M41 Solution Structure of the AXH domain of Ataxin-1 in complex with ligand peptide from Capicua Deposited 2013-01-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 34–48（15 aa） Fragment：Ataxin-1-binding linear motif (UNP 34-48)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；310 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Ataxin-1 AXH domain, 0.6 mM CIC polypeptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 15N] Ataxin-1 AXH domain, 0.6 mM CIC polypeptide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4J2J Crystal structure of AXH domain complex with Capicua Deposited 2013-02-04	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 D 28–48（21 aa） Fragment：UNP residues 28-48	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
4J2J Crystal structure of AXH domain complex with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 28–48（21 aa） Fragment：UNP residues 28-48	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
4J2J Crystal structure of AXH domain complex with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 28–48（21 aa） Fragment：UNP residues 28-48	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
4J2L Crystal Structure of AXH domain complexed with Capicua Deposited 2013-02-04	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 C 21–48（28 aa） Fragment：UNP residues 21-48	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.294
4J2L Crystal Structure of AXH domain complexed with Capicua Deposited 2013-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 21–48（28 aa） Fragment：UNP residues 21-48	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.294
6KZG 14-3-3 protein in Complex with CIC S301 phosphorylated peptide Deposited 2019-09-24	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 C 298–305（8 aa） Chain Q 298–305（8 aa）	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；293 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3350	Resolution 2.00 Å R-free 0.231
6KZH 14-3-3 protein in Complex with CIC S173 phosphorylated peptide Deposited 2019-09-24	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 C 170–177（8 aa） Chain Q 170–177（8 aa）	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；293 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.65 Å R-free 0.274
7M5W Crystal structure of the HMG-C1 domain of human capicua bound to DNA Deposited 2021-03-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 188–280（93 aa） Fragment：HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527 Chain A 1457–1527（71 aa） Fragment：HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；100 mM MES, 100 mM CaCl2, 100 mM NaCl, and 16% (w/v) PEG 8000	Resolution 2.95 Å R-free 0.243

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

View Construct and Data Evidence

UniProt name	CIC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–80； UniProt 199–276 Author chain D； PDBConstruct 3–80； UniProt 199–276 Author chain G； PDBConstruct 3–80； UniProt 199–276 Author chain J； PDBConstruct 3–80； UniProt 199–276

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	6jrp
Deposition date deposition_date	2019-04-05
Structure title title	Crystal structure of CIC-HMG-ETV5-DNA complex
Keywords keywords	repressor, protein-DNA complex, TRANSCRIPTION; 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	32.87 Å
Radius of gyration Rg (electron density) rg_electron	33.07 Å
Forward intensity I(0) i0	102558000.00
Molecular weight molecular_weight	63526.0 kDa
Excluded volume excluded_volume	71936 Å³
Envelope volume envelope_volume	108410 Å³
Hydration-shell volume shell_volume	29390 Å³
Envelope diameter envelope_diameter	122.3 Å
Shell Rg shell_rg	37.20 Å
Envelope Rg envelope_rg	32.15 Å
Shape Rg shape_rg	33.07 Å
Total Rg total_rg	33.36 Å
Total atoms total_atoms	4360
Residues n_residues	376
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	116.8 Å
Rg (real space) rg_real	33.18 Å
Rg uncertainty (real space) rg_real_error	1.25 Å
I(0) (real space) i0_real	1.0260e+08
I(0) uncertainty (real space) i0_real_error	1.5030e+06
Rg (reciprocal space) rg_reciprocal	33.05 Å
I(0) (reciprocal space) i0_reciprocal	102500000.0000
Solution quality estimate total_estimate	0.8433
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.9 Å
Skewness Skewness skewness	0.494
Kurtosis Kurtosis kurtosis	-0.168
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3173000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.776; Smooth: 0.894

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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	Protein capicua homolog
Molecular weight formula_weight	9880.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	4360

GSHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKK

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APTPGPAPAPTPGPAPAPAP*A)-3') ;
Molecular weight formula_weight	3414.3 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,E,H,K

ATGAATGAAAA

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(TPTPTPTPCPAPTPTPCPAP*T)-3') ;
Molecular weight formula_weight	3289.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,F,I,L

TTTTCATTCAT

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6jrpA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	6jrpD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	6jrpG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	6jrpJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

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8. Citations (1)

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Unit-cell length a length_a	66.082 Å
Unit-cell length b length_b	66.082 Å
Unit-cell length c length_c	158.285 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	12

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	38.791 Å
R factor r_factor	0.3006
R_work r_work	0.2968
R_free r_free	0.3343

fit	/app/data/saxs_computation/jr/6jrp/6jrp.fit
pddf	/app/data/pr_computation/jr/6jrp/6jrp.pr.out
profile	/app/data/saxs_computation/jr/6jrp/6jrp.dat

Crystal structure of CIC-HMG-ETV5-DNA complex

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

Protein capicua homolog

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 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)