SAXSdb — 8j9q

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

E3 ubiquitin-protein ligase UBR4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1660–1729	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350)	Resolution 2.18 Å R-free 0.269
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1660–1729	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350)	Resolution 2.18 Å R-free 0.269
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1660–1729	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350)	Resolution 2.18 Å R-free 0.269

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 8J9Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8J9R Crystal structure of UBR box of YIFS-UBR4 Deposited 2023-05-04	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1660–1729（70 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Bis-Tris (pH5.6), 29% (w/v) polyethylene glycol 3350 (PEG3350), 0.2 M lithium sulfate monohydrate	Resolution 1.65 Å R-free 0.287
9D9Z Structure of human UBR4-KCMF1-CaM E3 ligase complex (Silencing Factor of the Integrated stress response, SiFI) Deposited 2024-08-21	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 × 6 PDB declaration: hexameric	Chain A 2–5183（5182 aa） Chain B 2–5183（5182 aa）	Not recorded	ZN ZINC ION × 20 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9HXW Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (composite map) Deposited 2025-01-08	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 × 6 PDB declaration: hexameric	Chain A 1–4781（4781 aa） Chain B 1–4781（4781 aa）	Not recorded	ZN ZINC ION × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9NWD Human E3 ligase UBR4-KCMF1-calmodulin complex (N-terminal) Deposited 2025-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–5183（5183 aa） Chain B 1–5183（5183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9NWE E3 ligase UBR4-KCMF1-calmodulin complex Deposited 2025-03-22	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 × 6 PDB declaration: hexameric	Chain A 2–5183（5182 aa） Chain B 2–5183（5182 aa）	Not recorded	ZN ZINC ION × 6 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9QWS Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term dimer interface focused refinement) Deposited 2025-04-15	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 × 6 PDB declaration: hexameric	Chain A 1–5183（5183 aa） Chain B 1–5183（5183 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9QWU Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (CALM1 focused refinement) Deposited 2025-04-15	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 × 6 PDB declaration: hexameric	Chain A 1–5183（5183 aa） Chain B 1–5183（5183 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9QWX Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (N-term focused refinement) Deposited 2025-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–5183（5183 aa） Chain B 1–5183（5183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9QWZ Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (BP focused refinement) Deposited 2025-04-15	Different construct 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 B 1–5183（5183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
9QX0 Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term focused refinement) Deposited 2025-04-15	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 × 5 PDB declaration: pentameric	Chain A 1–5183（5183 aa） Chain B 1–5183（5183 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBR4_HUMAN
Isoform	Q5T4S7-5
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–73； UniProt 1660–1729 Author chain B； PDBConstruct 4–73； UniProt 1660–1729 Author chain C； PDBConstruct 4–73； UniProt 1660–1729

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	8j9q
Deposition date deposition_date	2023-05-04
Structure title title	Crystal structure of UBR box of UBR4 apo
Keywords keywords	E3 ligase, UBR box, LIGASE; 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	20.88 Å
Radius of gyration Rg (electron density) rg_electron	20.24 Å
Forward intensity I(0) i0	12906900.00
Molecular weight molecular_weight	25005.0 kDa
Excluded volume excluded_volume	30268 Å³
Envelope volume envelope_volume	38458 Å³
Hydration-shell volume shell_volume	16441 Å³
Envelope diameter envelope_diameter	68.0 Å
Shell Rg shell_rg	25.75 Å
Envelope Rg envelope_rg	20.08 Å
Shape Rg shape_rg	20.30 Å
Total Rg total_rg	20.80 Å
Total atoms total_atoms	1699
Residues n_residues	219
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	66.4 Å
Rg (real space) rg_real	20.81 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.2910e+07
I(0) uncertainty (real space) i0_real_error	1.7370e+05
Rg (reciprocal space) rg_reciprocal	20.83 Å
I(0) (reciprocal space) i0_reciprocal	12910000.0000
Solution quality estimate total_estimate	0.9034
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.7 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.717
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1361000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.999

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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	E3 ubiquitin-protein ligase UBR4
Molecular weight formula_weight	8238.6 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1754

GHMKLCTFTITQKEFMNQHWYHCHTCKMVDGVGVCTVCAKVCHKDHEISYAKYGSFFCDCGAKEDGSCLALVK

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	55

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8. Citations (1)

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Unit-cell length a length_a	43.670 Å
Unit-cell length b length_b	80.750 Å
Unit-cell length c length_c	81.320 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	12

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

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	29.760 Å
R factor r_factor	0.2217
R_work r_work	0.2192
R_free r_free	0.2688

fit	/app/data/saxs_computation/j9/8j9q/8j9q.fit
pddf	/app/data/pr_computation/j9/8j9q/8j9q.pr.out
profile	/app/data/saxs_computation/j9/8j9q/8j9q.dat

Crystal structure of UBR box of UBR4 apo

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

E3 ubiquitin-protein ligase UBR4

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