SAXSdb — 3a1q

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

Ubiquitin

Mus musculus

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–76 Chain B； UniProt 1–76	Mutation：77D Mutation：K63R	Ubiquitin interaction motif-containing protein 1 × 1 （Q5U5Q9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM Tris-HCl(pH8.5), 32% PEG4000, 200mM sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.268
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1–76 Chain E； UniProt 1–76	Mutation：77D Mutation：K63R	Ubiquitin interaction motif-containing protein 1 × 1 （Q5U5Q9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM Tris-HCl(pH8.5), 32% PEG4000, 200mM sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.268

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 3A1Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZNV Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer Deposited 2008-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–76（76 aa）	Mutation：K63R	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
2ZNV Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer Deposited 2008-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Mutation：M77D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
2ZNV Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer Deposited 2008-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–76（76 aa）	Mutation：K63R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
2ZNV Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer Deposited 2008-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–76（76 aa）	Mutation：M77D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
3A9J Crystal structure of the mouse TAB2-NZF in complex with Lys63-linked di-ubiquitin Deposited 2009-10-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Mutation：K63R Mutation：77D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；90mM Bis-Tris-HCl (pH 6.5), 180mM ammonium acetate, 21% PE3350, 4% pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.18 Å R-free 0.191
3A9K Crystal structure of the mouse TAB3-NZF in complex with Lys63-linked di-ubiquitin Deposited 2009-10-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Mutation：K63R Mutation：77D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bis-Tris-HCl (pH 6.5), 21% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.40 Å R-free 0.218

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

View Construct and Data Evidence

UniProt name	UBIQ_MOUSE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76

Ubiquitin interaction motif-containing protein 1

Mus musculus

UniProt Q5U5Q9

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 80–120	Fragment：UNP residues 80-120	Ubiquitin × 1 （P62991） Ubiquitin × 1 （P62991）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM Tris-HCl(pH8.5), 32% PEG4000, 200mM sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.268
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 80–120	Fragment：UNP residues 80-120	Ubiquitin × 1 （P62991） Ubiquitin × 1 （P62991）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100mM Tris-HCl(pH8.5), 32% PEG4000, 200mM sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.268

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 3A1Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GVW Crystal structure of the BRCA1-A complex Deposited 2018-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain E 275–334（60 aa） Chain J 275–334（60 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；100 mM MES-KOH pH 5.6, 200 mM MgCl2, 8% (w/v) PEG6000	Resolution 3.75 Å R-free 0.259

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

View Construct and Data Evidence

UniProt name	UIMC1_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–45； UniProt 80–120 Author chain F； PDBConstruct 5–45； UniProt 80–120

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	3a1q
Deposition date deposition_date	2009-04-21
Structure title title	Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin
Keywords keywords	;protein complex, Cytoplasm, Nucleus, Phosphoprotein, Ubl conjugation, Transcription regulation, GENE REGULATION-SIGNALING PROTEIN COMPLEX ;; GENE REGULATION/SIGNALING PROTEIN
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	27.15 Å
Radius of gyration Rg (electron density) rg_electron	26.20 Å
Forward intensity I(0) i0	33136400.00
Molecular weight molecular_weight	43999.0 kDa
Excluded volume excluded_volume	55168 Å³
Envelope volume envelope_volume	73117 Å³
Hydration-shell volume shell_volume	24011 Å³
Envelope diameter envelope_diameter	84.6 Å
Shell Rg shell_rg	32.49 Å
Envelope Rg envelope_rg	25.89 Å
Shape Rg shape_rg	26.19 Å
Total Rg total_rg	26.96 Å
Total atoms total_atoms	3091
Residues n_residues	389
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	83.4 Å
Rg (real space) rg_real	27.04 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	3.3140e+07
I(0) uncertainty (real space) i0_real_error	5.0400e+05
Rg (reciprocal space) rg_reciprocal	27.08 Å
I(0) (reciprocal space) i0_reciprocal	33140000.0000
Solution quality estimate total_estimate	0.7392
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	38.8 Å
Skewness Skewness skewness	0.085
Kurtosis Kurtosis kurtosis	-0.674
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9073000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 0.998; Smooth: 0.986

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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	Ubiquitin
Molecular weight formula_weight	8691.9 kDa
Mutation mutation	77D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	3247

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8604.8 kDa
Mutation mutation	K63R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin interaction motif-containing protein 1
Molecular weight formula_weight	5080.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPLGSEEEQFALALKMSEQEAREVNNQEEKEEELLRKAIAESLNS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	156

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3a1qa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3a1qb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3a1qd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3a1qe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (4 domains)

Domain ID domain_id	3a1qA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3a1qB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3a1qD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	3a1qE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	65.235 Å
Unit-cell length b length_b	74.810 Å
Unit-cell length c length_c	83.031 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	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	42.310 Å
R factor r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2680

fit	/app/data/saxs_computation/a1/3a1q/3a1q.fit
pddf	/app/data/pr_computation/a1/3a1q/3a1q.pr.out
profile	/app/data/saxs_computation/a1/3a1q/3a1q.dat

Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin interaction motif-containing protein 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

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)