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9m3i

Crystal structure of the Bre1-Lge1 complex

Method: X-RAY DIFFRACTION Dmax: 240.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 313–700 Chain B； UniProt 313–700 Chain D； UniProt 227–312 Chain E； UniProt 227–312 Not recorded Transcriptional regulatory protein LGE1 × 1 （Q02796） 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

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 9M3I 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
7UV8 Rad6-Bre1 Complex Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state 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；286.15 K；0.05 to 0.1 M MMT buffer and 15-25% PEG400
Resolution 2.70 Å R-free 0.280
7UVC Rad6(P43L)-Bre1 Complex Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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

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 1, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–388； UniProt 313–700 Author chain B； PDBConstruct 1–388； UniProt 313–700 Author chain D； PDBConstruct 1–86； UniProt 227–312 Author chain E； PDBConstruct 1–86； UniProt 227–312

Transcriptional regulatory protein LGE1

Saccharomyces cerevisiae S288C

UniProt Q02796

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain C； UniProt 261–332 Not recorded E3 ubiquitin-protein ligase BRE1 × 2 （Q07457） E3 ubiquitin-protein ligase BRE1 × 2 （Q07457） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name LGE1_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–72； UniProt 261–332

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9m3i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9m3i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9m3i
Deposition date deposition_date2025-03-02
Structure title titleCrystal structure of the Bre1-Lge1 complex
Keywords keywordsubiquitin ligase, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier74.25 Å
Radius of gyration Rg (electron density) rg_electron76.31 Å
Forward intensity I(0) i0128208000.00
Molecular weight molecular_weight92469.0 kDa
Excluded volume excluded_volume115630 ų
Envelope volume envelope_volume202200 ų
Hydration-shell volume shell_volume29212 ų
Envelope diameter envelope_diameter269.7 Å
Shell Rg shell_rg46.83 Å
Envelope Rg envelope_rg77.44 Å
Shape Rg shape_rg76.38 Å
Total Rg total_rg75.15 Å
Total atoms total_atoms6491
Residues n_residues799
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax240.6 Å
Rg (real space) rg_real74.76 Å
Rg uncertainty (real space) rg_real_error2.76 Å
I(0) (real space) i0_real1.2780e+08
I(0) uncertainty (real space) i0_real_error3.2580e+06
Rg (reciprocal space) rg_reciprocal68.94 Å
I(0) (reciprocal space) i0_reciprocal126500000.0000
Solution quality estimate total_estimate0.6004
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.9 Å
Skewness Skewness skewness0.598
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0058
Highest regularization parameter α highest_alpha4709000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.070; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 0.135; Smooth: 0.491
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)