SAXSdb — 9hfu

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

Speckle type BTB/POZ protein

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 28–166	Not recorded	Caprin-1 × 1 （Q14444）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.204
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 28–166	Not recorded	Caprin-1 × 1 （Q14444） NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.204

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 9HFU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7KPI Crystal structure of the SPOP MATH domain Deposited 2020-11-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M HEPES, pH 7.5, 23% (w/v) PME 550, 5 mM DTT	Resolution 1.70 Å R-free 0.196
7KPK Crystal structure of the SPOP MATH domain in complex with a fragment of Pdx1 Deposited 2020-11-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa） Fragment：MATH domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；50 mM sodium cacodylate, pH 6.5, 0.08 M magnesium acetate, 30% (w/v) PEG 4000	Resolution 1.71 Å R-free 0.227
9HFW SRC-3 (NCoA-3) peptide bound to SPOP MATH domain Deposited 2024-11-18	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.223
9HGH MyD88 peptide_1 bound to SPOP MATH domain Deposited 2024-11-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.90 Å R-free 0.232

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	D6RDG8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–141； UniProt 28–166 Author chain B； PDBConstruct 3–141； UniProt 28–166

Caprin-1

OrganismNot specified

UniProt Q14444

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 D； UniProt 426–442	Not recorded	Speckle type BTB/POZ protein × 1 （D6RDG8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.204
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 426–442	Not recorded	Speckle type BTB/POZ protein × 1 （D6RDG8） NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.70 Å R-free 0.204

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 9HFU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WBE Crystal structure of the HR-1 domain of human caprin-1 in the C121 space group Deposited 2014-09-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 132–251（120 aa） Fragment：unp residues 132-251	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG750MME, 0.1 M Tris, 0.1 M potassium fluoride, 10% glycerol	Resolution 2.05 Å R-free 0.231
4WBE Crystal structure of the HR-1 domain of human caprin-1 in the C121 space group Deposited 2014-09-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 132–251（120 aa） Fragment：unp residues 132-251 Chain C 132–251（120 aa） Fragment：unp residues 132-251	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；22% PEG750MME, 0.1 M Tris, 0.1 M potassium fluoride, 10% glycerol	Resolution 2.05 Å R-free 0.231
4WBP Crystal structure of the HR-1 domain of human caprin-1 in the P3121 space group Deposited 2014-09-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 132–251（120 aa） Fragment：unp residues 132-251 Chain B 132–251（120 aa） Fragment：unp residues 132-251	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, HANGING DROP；pH 8；298 K；12% PEG600, 0.1 M Tris, 0.1 M Calcium acetate, 10% glycerol	Resolution 2.50 Å R-free 0.266
6TA7 CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF Deposited 2019-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 356–386（31 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium chloride, 0.1M Tris 8.0, 20% w/v PEG 4000 of the Proplex crystallization screen (Molecular Dimensions)	Resolution 1.93 Å R-free 0.252
6TA7 CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF Deposited 2019-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 356–386（31 aa）	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium chloride, 0.1M Tris 8.0, 20% w/v PEG 4000 of the Proplex crystallization screen (Molecular Dimensions)	Resolution 1.93 Å R-free 0.252
8TH7 Crystal Structure of the G3BP1 NTF2-like domain bound to the Caprin1 peptide Deposited 2023-07-14	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 360–381（22 aa） Chain D 360–381（22 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；1.8M tri-ammonium citrate pH 7.0	Resolution 2.88 Å R-free 0.277

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

View Construct and Data Evidence

UniProt name	CAPR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–17； UniProt 426–442 Author chain D； PDBConstruct 1–17； UniProt 426–442

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	9hfu
Deposition date deposition_date	2024-11-18
Structure title title	Caprin1 peptide bound to SPOP MATH domain
Keywords keywords	Ubiquitination, Ligase, Complex, Degradation; LIGASE
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	21.82 Å
Radius of gyration Rg (electron density) rg_electron	20.58 Å
Forward intensity I(0) i0	19894700.00
Molecular weight molecular_weight	34864.0 kDa
Excluded volume excluded_volume	44120 Å³
Envelope volume envelope_volume	52702 Å³
Hydration-shell volume shell_volume	21379 Å³
Envelope diameter envelope_diameter	74.6 Å
Shell Rg shell_rg	26.93 Å
Envelope Rg envelope_rg	20.79 Å
Shape Rg shape_rg	20.55 Å
Total Rg total_rg	21.54 Å
Total atoms total_atoms	4874
Residues n_residues	311
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	72.5 Å
Rg (real space) rg_real	21.74 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	1.9890e+07
I(0) uncertainty (real space) i0_real_error	2.2640e+05
Rg (reciprocal space) rg_reciprocal	21.75 Å
I(0) (reciprocal space) i0_reciprocal	19890000.0000
Solution quality estimate total_estimate	0.8863
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.224
Kurtosis Kurtosis kurtosis	-0.454
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6442000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.964

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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	Speckle type BTB/POZ protein
Molecular weight formula_weight	16309.8 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	5160

APKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQD

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	Caprin-1
Molecular weight formula_weight	1792.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

QPEATQVPLVSSTSEGY

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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8. Citations (1)

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Unit-cell length a length_a	39.808 Å
Unit-cell length b length_b	60.882 Å
Unit-cell length c length_c	57.117 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	41.660 Å
R factor r_factor	0.1646
R_work r_work	0.1624
R_free r_free	0.2039

fit	/app/data/saxs_computation/hf/9hfu/9hfu.fit
pddf	/app/data/pr_computation/hf/9hfu/9hfu.pr.out
profile	/app/data/saxs_computation/hf/9hfu/9hfu.dat

Caprin1 peptide bound to SPOP MATH domain

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

Speckle type BTB/POZ protein

State in the Current Structure

Other States of the Same Protein in the Database

Caprin-1

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)