SAXSdb — 7uv8

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

Ubiquitin-conjugating enzyme E2 2

Saccharomyces cerevisiae S288C

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 1–150	Not recorded	E3 ubiquitin-protein ligase BRE1 × 2 （Q07457）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；286.15 K；0.05 to 0.1 M MMT buffer and 15-25% PEG400	Resolution 2.70 Å R-free 0.280

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 7UV8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AYZ CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION Deposited 1997-11-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–172（172 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 2.60 Å R-free 0.246
1AYZ CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION Deposited 1997-11-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–172（172 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 2.60 Å R-free 0.246
1AYZ CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION Deposited 1997-11-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–172（172 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 2.60 Å R-free 0.246
4R62 Structure of Rad6~Ub Deposited 2014-08-22	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 A 1–172（172 aa） Fragment：Rad6	Mutation：C88K	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；24% PEG 300, 50 mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.28 Å R-free 0.265
7MEX Structure of yeast Ubr1 in complex with Ubc2 and N-degron Deposited 2021-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 3–152（150 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
7MEY Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron Deposited 2021-04-08	Different construct 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 B 1–172（172 aa）	Not recorded	ZN ZINC ION × 7 Z3V 2-(ethylamino)ethane-1-thiol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
7UVC Rad6(P43L)-Bre1 Complex Deposited 2022-04-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–150（150 aa）	Mutation：P43L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；286 K；0.05 to 0.1 M MMT buffer and 15-25% PEG400	Resolution 3.05 Å R-free 0.279
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain R 3–150（148 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBC2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–150； UniProt 1–150

E3 ubiquitin-protein ligase BRE1

Saccharomyces cerevisiae S288C

UniProt Q07457

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 U； UniProt 1–212 Chain V； UniProt 1–212	Not recorded	Ubiquitin-conjugating enzyme E2 2 × 1 （P06104）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；286.15 K；0.05 to 0.1 M MMT buffer and 15-25% PEG400	Resolution 2.70 Å R-free 0.280

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 7UV8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4R7E Structure of Bre1 RING domain Deposited 2014-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 632–700（69 aa） Fragment：RING domain (UNP residues 632-700)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；2.0 M ammonium sulfate and 0.1 mM sodium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.25 Å R-free 0.247
7UVC Rad6(P43L)-Bre1 Complex Deposited 2022-04-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain U 1–212（212 aa） Chain V 1–212（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；286 K；0.05 to 0.1 M MMT buffer and 15-25% PEG400	Resolution 3.05 Å R-free 0.279
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain A 637–700（64 aa） Chain B 637–700（64 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
8T3T Structure of Bre1-nucleosome complex - state3 Deposited 2023-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 591–700（110 aa） Chain L 591–700（110 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8T3W Structure of Bre1-nucleosome complex - state2 Deposited 2023-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 591–700（110 aa） Chain L 591–700（110 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8T3Y Structure of Bre1-nucleosome complex - state1 Deposited 2023-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 591–700（110 aa） Chain L 591–700（110 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9M3I Crystal structure of the Bre1-Lge1 complex Deposited 2025-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 313–700（388 aa） Chain B 313–700（388 aa） Chain D 227–312（86 aa） Chain E 227–312（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；120 mM ammonium citrate (pH 7.0), 12 % polyethylene glycol monomethyl ether (molecular weight 5000 Da), 0.5% beta-mercaptoethanol and 20 mM dithiothreitol	Resolution 3.50 Å R-free 0.325

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BRE1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain U； PDBConstruct 1–212； UniProt 1–212 Author chain V； PDBConstruct 1–212； UniProt 1–212

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	7uv8
Deposition date deposition_date	2022-04-29
Structure title title	Rad6-Bre1 Complex
Keywords keywords	E2 conjugation, E3 Ligase, LIGASE, TRANSFERASE-LIGASE complex; TRANSFERASE/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	34.20 Å
Radius of gyration Rg (electron density) rg_electron	34.52 Å
Forward intensity I(0) i0	48234600.00
Molecular weight molecular_weight	54922.0 kDa
Excluded volume excluded_volume	68729 Å³
Envelope volume envelope_volume	89448 Å³
Hydration-shell volume shell_volume	24249 Å³
Envelope diameter envelope_diameter	120.2 Å
Shell Rg shell_rg	36.37 Å
Envelope Rg envelope_rg	34.22 Å
Shape Rg shape_rg	34.48 Å
Total Rg total_rg	34.78 Å
Total atoms total_atoms	3861
Residues n_residues	470
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	120.2 Å
Rg (real space) rg_real	34.65 Å
Rg uncertainty (real space) rg_real_error	1.25 Å
I(0) (real space) i0_real	4.8230e+07
I(0) uncertainty (real space) i0_real_error	7.2630e+05
Rg (reciprocal space) rg_reciprocal	34.37 Å
I(0) (reciprocal space) i0_reciprocal	48220000.0000
Solution quality estimate total_estimate	0.7358
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.546
Kurtosis Kurtosis kurtosis	-0.555
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5947000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.463; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.362; Smooth: 0.810

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-conjugating enzyme E2 2
Molecular weight formula_weight	17191.5 kDa
EC 编号 ec_number	2.3.2.23
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	3861

MSTPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWE

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase BRE1
Molecular weight formula_weight	24834.0 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V,U

MTAEPATKKIKLELSDPSEPLTQSDVIAFQKEALFRCINRRRVDFEALRKQYELSRRECIDVSRKLANIMALIVTLARFIETFCTDANEKQLCREIAQGDETLIVQRSDSFMKLLTKYGKPNTTDSNTNSNASDHIQELTTELKNLRKSKEELFYENSQLTEEISALKEYYTNIIRKYDRDESFTIKRVFKEDKTDAVKELREDEKESNENN

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	241.580 Å
Unit-cell length b length_b	49.951 Å
Unit-cell length c length_c	57.568 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	38.490 Å
R factor r_factor	0.2420
R_work r_work	0.2400
R_free r_free	0.2800

fit	/app/data/saxs_computation/uv/7uv8/7uv8.fit
pddf	/app/data/pr_computation/uv/7uv8/7uv8.pr.out
profile	/app/data/saxs_computation/uv/7uv8/7uv8.dat

Rad6-Bre1 Complex

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

Ubiquitin-conjugating enzyme E2 2

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin-protein ligase BRE1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)