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8j1r

cryo-EM structures of Ufd4 in complex with Ubc4-Ub

Method: ELECTRON MICROSCOPY Dmax: 110.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin fusion degradation protein 4

Saccharomyces cerevisiae

UniProt P33202

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–1483 Not recorded Ubiquitin-conjugating enzyme E2 4 × 1 （P15731） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.52 Å

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 8J1R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8J1P Cryo-EM structure of Ufd4 in complex with K29/48 triUb Deposited 2023-04-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1483（1483 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å

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

View Construct and Data Evidence
UniProt name UFD4_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1483； UniProt 1–1483

Ubiquitin-conjugating enzyme E2 4

Saccharomyces cerevisiae

UniProt P15731

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–148 Mutation：C22S,C108S Ubiquitin fusion degradation protein 4 × 1 （P33202） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.52 Å

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 8J1R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1QCQ UBIQUITIN CONJUGATING ENZYME Deposited 1999-05-10 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–148（148 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；PEG 8000, MAGNESIUM ACETATE, CACODYLATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP
Resolution 2.70 Å R-free 0.296
5AIE Not4 ring domain in complex with Ubc4 Deposited 2015-02-12 Different mutation/modification 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 1–148（148 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；10% (W/V) PEG 8000, 0.02 M OF L-NA-GLUTAMATE, 0.02 M OF ALANINE (RACEMIC), 0.02 M OF GLYCINE, 0.02 M OF LYSINE HCL (RACEMIC), 0.02 M OF SERINE (RACEMIC), 0.1 M BICINE PH 8.5 AND 20% (W/V) ETHYLENE GLYCOL AS CRYSTALLIZATION BUFFER AT ROOM TEMPERATURE.
Resolution 2.80 Å R-free 0.271
9KHS Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation) Deposited 2024-11-11 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–148（148 aa）
Mutation：C22S/C102S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
9KHT cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation) Deposited 2024-11-11 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain B 1–148（148 aa）
Chain b 1–148（148 aa）
Mutation：C22S/C108S Mutation：C22S/C108S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.85 Å
9M7O Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation) Deposited 2025-03-10 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–148（148 aa）
Mutation：C22S/C102S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBC4_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–148； UniProt 1–148

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 8j1r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8j1r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8j1r
Deposition date deposition_date2023-04-13
Structure title titlecryo-EM structures of Ufd4 in complex with Ubc4-Ub
Keywords keywordsUfd4, Ubc4, Ubc4-Ub, HECT-type E3 ligase, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.34 Å
Radius of gyration Rg (electron density) rg_electron32.52 Å
Forward intensity I(0) i0124535000.00
Molecular weight molecular_weight92061.0 kDa
Excluded volume excluded_volume116570 ų
Envelope volume envelope_volume150810 ų
Hydration-shell volume shell_volume39545 ų
Envelope diameter envelope_diameter115.8 Å
Shell Rg shell_rg38.45 Å
Envelope Rg envelope_rg32.22 Å
Shape Rg shape_rg32.51 Å
Total Rg total_rg33.05 Å
Total atoms total_atoms6497
Residues n_residues823
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 dmax110.4 Å
Rg (real space) rg_real33.32 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real1.2450e+08
I(0) uncertainty (real space) i0_real_error1.8970e+06
Rg (reciprocal space) rg_reciprocal33.34 Å
I(0) (reciprocal space) i0_reciprocal124500000.0000
Solution quality estimate total_estimate0.6667
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.6 Å
Skewness Skewness skewness0.314
Kurtosis Kurtosis kurtosis-0.239
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49760000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.983; Smooth: 0.864
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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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8. Citations (1)

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9. Files and Curves (10)