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3m62

Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23

Method: X-RAY DIFFRACTION Dmax: 158.1 Å Quality: REASONABLE
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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–961 Mutation：S102L, D677V UV excision repair protein RAD23 × 1 （P32628） 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

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 3M62 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 oligomeric state 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
2QJ0 Structure of the yeast U-box-containing ubiquitin ligase Ufd2p Deposited 2007-07-06 Different mutation/modification Different oligomeric state 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 Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule 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
3M63 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2 Deposited 2010-03-15 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 8–968； UniProt 1–961

UV excision repair protein RAD23

Saccharomyces cerevisiae

UniProt P32628

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 B； UniProt 1–84 Fragment：UNP residues 1-84, Ubiquitin-like domain Ubiquitin conjugation factor E4 × 1 （P54860） 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

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 3M62 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1X3W Structure of a peptide:N-glycanase-Rad23 complex Deposited 2005-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 238–309（72 aa） Fragment：XPC binding domain
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；sodium chloride, MES, pH 6, VAPOR DIFFUSION, temperature 291K
Resolution 3.00 Å R-free 0.274
1X3Z Structure of a peptide:N-glycanase-Rad23 complex Deposited 2005-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 238–309（72 aa） Fragment：XPC binding domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；sodium chloride, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.270
2NBU Solution structure of the Rad23 ubiquitin-like (UBL) domain Deposited 2016-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–78（78 aa） Fragment：residues 1-78
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N] shuttling protein, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N] shuttling protein, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
2NBW Solution structure of the Rpn1 T1 site with the Rad23 UBL domain Deposited 2016-03-14 Different construct 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 1–78（78 aa） Fragment：residues 1-78
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.04-0.6 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM protein_1, 0.6 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
2QSF Crystal structure of the Rad4-Rad23 complex Deposited 2007-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 230–398（169 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM sodium phosphate, 8% (w/v) PEG 2000, 2 mM dithiothreitol, pH 6.5, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.245
2QSG Crystal structure of Rad4-Rad23 bound to a UV-damaged DNA Deposited 2007-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain X 230–398（169 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100mM sodium chloride, 6% (v/v) isopropanol, 14 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Resolution 3.10 Å R-free 0.277
2QSH Crystal structure of Rad4-Rad23 bound to a mismatch DNA Deposited 2007-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain X 230–398（169 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100 mM sodium chloride, 15% (v/v) isopropanol, 10 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.81 Å R-free 0.244
3ESW Complex of yeast PNGase with GlcNAc2-IAc. Deposited 2008-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 254–308（55 aa） Fragment：XPCB Domain
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；291 K；0.1 M Tris-HCl, pH 8.5 and 2.0 M sodium chloride, EVAPORATION, temperature 291K
Resolution 3.40 Å R-free 0.235
4YIR Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA Deposited 2015-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain X 230–398（169 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50mM BTP-HCl, 100mM NaCl, 14% isopropanol and 100mM calcium chloride
Resolution 3.05 Å R-free 0.253
6CFI Crystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion Deposited 2018-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain X 230–398（169 aa） Fragment：residues 230-398
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；bis-tris propane 5 mM sodium chloride 100 mM 1-propanol 14% spermidine-HCl 5 mM dithiothreitol 5 mM
Resolution 3.36 Å R-free 0.268
6UBF Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain X 230–398（169 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol
Resolution 4.60 Å R-free 0.356
6UG1 Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain X 256–311（56 aa） Fragment：UNP residues 256-311
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride
Resolution 2.83 Å R-free 0.272
6UIN Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain X 230–398（169 aa） Fragment：UNP residues 230-398
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 200 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride
Resolution 3.35 Å R-free 0.262

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAD23_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–84； UniProt 1–84

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 3m62

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3m62
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3m62
Deposition date deposition_date2010-03-15
Structure title titleCrystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23
Keywords keywordsArmadillo-like repeats, Ubl conjugation pathway, DNA damage, DNA repair, Nucleus, Phosphoprotein, LIGASE-PROTEIN BINDING complex; LIGASE/PROTEIN BINDING
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_guinier42.00 Å
Radius of gyration Rg (electron density) rg_electron42.17 Å
Forward intensity I(0) i0197010000.00
Molecular weight molecular_weight117590.0 kDa
Excluded volume excluded_volume148760 ų
Envelope volume envelope_volume209150 ų
Hydration-shell volume shell_volume45663 ų
Envelope diameter envelope_diameter166.2 Å
Shell Rg shell_rg41.50 Å
Envelope Rg envelope_rg43.13 Å
Shape Rg shape_rg42.12 Å
Total Rg total_rg42.30 Å
Total atoms total_atoms8289
Residues n_residues1027
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 dmax158.1 Å
Rg (real space) rg_real42.56 Å
Rg uncertainty (real space) rg_real_error1.95 Å
I(0) (real space) i0_real1.9700e+08
I(0) uncertainty (real space) i0_real_error3.6590e+06
Rg (reciprocal space) rg_reciprocal42.01 Å
I(0) (reciprocal space) i0_reciprocal196900000.0000
Solution quality estimate total_estimate0.5507
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.5 Å
Skewness Skewness skewness0.710
Kurtosis Kurtosis kurtosis0.105
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24980000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.552; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.681; Smooth: 0.792
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3m62b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3m62A02
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)
Domain ID domain_id3m62B00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)