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1ayz

CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 119.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

UBIQUITIN-CONJUGATING ENZYME RAD6

OrganismNot specified

UniProt P06104

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 1–172 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；pH 5.0 Resolution 2.60 Å R-free 0.246
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–172 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；pH 5.0 Resolution 2.60 Å R-free 0.246
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–172 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；pH 5.0 Resolution 2.60 Å R-free 0.246

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 1AYZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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
7UV8 Rad6-Bre1 Complex Deposited 2022-04-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–150（150 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 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 6 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 1–169； UniProt 1–172 Author chain B； PDBConstruct 1–169； UniProt 1–172 Author chain C； PDBConstruct 1–169； UniProt 1–172

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 1ayz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ayz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ayz
Deposition date deposition_date1997-11-12
Structure title titleCRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION
Keywords keywordsUBIQUITIN CONJUGATION, UBIQUITIN-CONJUGATING ENZYME; UBIQUITIN CONJUGATION
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_guinier43.94 Å
Radius of gyration Rg (electron density) rg_electron43.34 Å
Forward intensity I(0) i041867500.00
Molecular weight molecular_weight52478.0 kDa
Excluded volume excluded_volume65434 ų
Envelope volume envelope_volume108420 ų
Hydration-shell volume shell_volume20979 ų
Envelope diameter envelope_diameter121.7 Å
Shell Rg shell_rg50.31 Å
Envelope Rg envelope_rg39.60 Å
Shape Rg shape_rg43.35 Å
Total Rg total_rg43.68 Å
Total atoms total_atoms3696
Residues n_residues459
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 dmax119.0 Å
Rg (real space) rg_real43.76 Å
Rg uncertainty (real space) rg_real_error1.05 Å
I(0) (real space) i0_real4.1870e+07
I(0) uncertainty (real space) i0_real_error7.1960e+05
Rg (reciprocal space) rg_reciprocal43.94 Å
I(0) (reciprocal space) i0_reciprocal41880000.0000
Solution quality estimate total_estimate0.6131
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary72.8 Å
Skewness Skewness skewness-0.343
Kurtosis Kurtosis kurtosis-1.169
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1245000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.043; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.666; Smooth: 0.170
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1ayza_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd1ayzb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd1ayzc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related

CATH v4.4 (3 domains)

Domain ID domain_id1ayzA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id1ayzB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id1ayzC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
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8. Citations (1)

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9. Files and Curves (10)