SAXSdb — 7m5w

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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 188–280 Chain A； UniProt 1457–1527	Fragment：HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527	;DNA (5'-D(GPGPTPTPAPTPGPAPAPTPGPAPAPAPAPAPGPC)-3') ; × 1 ;DNA (5'-D(GPCPTPTPTPTPTPCPAPTPTPCPAPTPAPAPCPC)-3') ; × 1 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

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 7M5W	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
6JRP Crystal structure of CIC-HMG-ETV5-DNA complex Deposited 2019-04-05	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 199–276（78 aa）	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, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334
6JRP Crystal structure of CIC-HMG-ETV5-DNA complex Deposited 2019-04-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 199–276（78 aa）	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, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334
6JRP Crystal structure of CIC-HMG-ETV5-DNA complex Deposited 2019-04-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 199–276（78 aa）	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, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334
6JRP Crystal structure of CIC-HMG-ETV5-DNA complex Deposited 2019-04-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain J 199–276（78 aa）	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, HANGING DROP；293 K；Ammonium acetate, PEG3350, Bis-tris pH 6.5	Resolution 3.00 Å R-free 0.334
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 ligand/ion 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 ligand/ion 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

6 other PDB entries and 12 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 22–114； UniProt 188–280 Author chain A； PDBConstruct 116–186； UniProt 1457–1527

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	7m5w
Deposition date deposition_date	2021-03-25
Structure title title	Crystal structure of the HMG-C1 domain of human capicua bound to DNA
Keywords keywords	helix-turn-helix, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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	19.70 Å
Radius of gyration Rg (electron density) rg_electron	18.98 Å
Forward intensity I(0) i0	20659000.00
Molecular weight molecular_weight	27537.0 kDa
Excluded volume excluded_volume	31425 Å³
Envelope volume envelope_volume	40660 Å³
Hydration-shell volume shell_volume	18165 Å³
Envelope diameter envelope_diameter	64.0 Å
Shell Rg shell_rg	24.92 Å
Envelope Rg envelope_rg	19.34 Å
Shape Rg shape_rg	18.94 Å
Total Rg total_rg	19.78 Å
Total atoms total_atoms	1897
Residues n_residues	174
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	64.0 Å
Rg (real space) rg_real	19.62 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.0660e+07
I(0) uncertainty (real space) i0_real_error	2.3210e+05
Rg (reciprocal space) rg_reciprocal	19.64 Å
I(0) (reciprocal space) i0_reciprocal	20660000.0000
Solution quality estimate total_estimate	0.8959
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.1 Å
Skewness Skewness skewness	0.214
Kurtosis Kurtosis kurtosis	-0.439
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3276000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein capicua homolog
Molecular weight formula_weight	21962.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1912

MGSSHHHHHHSSGLVPRGSHMDGRSPNKREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKKSSSEFKVPYSSLRRTLDQRRALVMQLFQDHGFFPSAQATAAFQARYADIFPSKVCLQLKIREVRQKIMQAATPTEQ

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 2 Entity 2 polymer

Description description	;DNA (5'-D(GPGPTPTPAPTPGPAPAPTPGPAPAPAPAPAPGPC)-3') ;
Molecular weight formula_weight	5612.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

GGTTATGAATGAAAAAGC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPCPTPTPTPTPTPCPAPTPTPCPAPTPAPAPCPC)-3') ;
Molecular weight formula_weight	5416.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GCTTTTTCATTCATAACC

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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8. Citations (2)

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Unit-cell length a length_a	46.890 Å
Unit-cell length b length_b	79.920 Å
Unit-cell length c length_c	106.960 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	23.840 Å
R factor r_factor	0.2111
R_work r_work	0.2093
R_free r_free	0.2434

fit	/app/data/saxs_computation/m5/7m5w/7m5w.fit
pddf	/app/data/pr_computation/m5/7m5w/7m5w.pr.out
profile	/app/data/saxs_computation/m5/7m5w/7m5w.dat

Crystal structure of the HMG-C1 domain of human capicua bound to DNA

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)