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2qj0

Structure of the yeast U-box-containing ubiquitin ligase Ufd2p

Method: X-RAY DIFFRACTION Dmax: 150.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin conjugation factor E4

Saccharomyces cerevisiae

UniProt P54860

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 1–961 Mutation：S102L, D677V Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；20% PEG 3350, 0.3M tri-ammonium citrate (pH 7.2), 0.1M sodium chloride, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.65 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 2QJ0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2QIZ Structure of the yeast U-box-containing ubiquitin ligase Ufd2p Deposited 2007-07-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–961（961 aa）
Mutation：S102L, D677V K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；20% PEG 3350, 0.2M tri-potassium citrate, 5mM DTT, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.56 Å R-free 0.276
3M62 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23 Deposited 2010-03-15 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 1–961（961 aa）
Mutation：S102L, D677V 1PE PENTAETHYLENE GLYCOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.257
3M63 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2 Deposited 2010-03-15 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 1–961（961 aa）
Mutation：S102L, D677V 1PE PENTAETHYLENE GLYCOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.270
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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–961（961 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 1–955（955 aa）
Chain a 1–955（955 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.85 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–961（961 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å

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

View Construct and Data Evidence
UniProt name UFD2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–982； UniProt 1–961

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 2qj0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qj0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qj0
Deposition date deposition_date2007-07-06
Structure title titleStructure of the yeast U-box-containing ubiquitin ligase Ufd2p
Keywords keywordshelical hairpin, LIGASE; LIGASE
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_guinier39.23 Å
Radius of gyration Rg (electron density) rg_electron39.60 Å
Forward intensity I(0) i0171721000.00
Molecular weight molecular_weight108100.0 kDa
Excluded volume excluded_volume135980 ų
Envelope volume envelope_volume185390 ų
Hydration-shell volume shell_volume43069 ų
Envelope diameter envelope_diameter159.5 Å
Shell Rg shell_rg40.05 Å
Envelope Rg envelope_rg40.57 Å
Shape Rg shape_rg39.56 Å
Total Rg total_rg39.79 Å
Total atoms total_atoms7567
Residues n_residues919
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 dmax150.8 Å
Rg (real space) rg_real39.97 Å
Rg uncertainty (real space) rg_real_error2.00 Å
I(0) (real space) i0_real1.7170e+08
I(0) uncertainty (real space) i0_real_error3.4170e+06
Rg (reciprocal space) rg_reciprocal39.51 Å
I(0) (reciprocal space) i0_reciprocal171600000.0000
Solution quality estimate total_estimate0.7586
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.7 Å
Skewness Skewness skewness0.761
Kurtosis Kurtosis kurtosis0.332
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21580000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.521; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.521; Smooth: 0.773
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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2qj0A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (10)