7nw1

Crystal structure of UFC1 in complex with UBA5

Method: X-RAY DIFFRACTION Dmax: 91.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-fold modifier-conjugating enzyme 1

Homo sapiens

UniProt Q9Y3C8

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 AAA; UniProt 1–167 Not recorded Ubiquitin-like modifier-activating enzyme 5 × 1 (Q9GZZ9) EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride Resolution 1.95 Å R-free 0.280
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain BBB; UniProt 1–167 Not recorded Ubiquitin-like modifier-activating enzyme 5 × 1 (Q9GZZ9) EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride Resolution 1.95 Å R-free 0.280

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.

26 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UFC1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain AAA; PDBConstruct 2–168; UniProt 1–167 Author chain BBB; PDBConstruct 2–168; UniProt 1–167

Ubiquitin-like modifier-activating enzyme 5

Homo sapiens

UniProt Q9GZZ9

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 FFF; UniProt 389–404 Not recorded Ubiquitin-fold modifier-conjugating enzyme 1 × 1 (Q9Y3C8) EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride Resolution 1.95 Å R-free 0.280
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain CCC; UniProt 389–404 Not recorded Ubiquitin-fold modifier-conjugating enzyme 1 × 1 (Q9Y3C8) EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride Resolution 1.95 Å R-free 0.280

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.

9 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBA5_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain CCC; PDBConstruct 1–16; UniProt 389–404 Author chain FFF; PDBConstruct 1–16; UniProt 389–404

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 7nw1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7nw1
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7nw1
Deposition date deposition_date2021-03-16
Structure title titleCrystal structure of UFC1 in complex with UBA5
Keywords keywords;Ubiquitin like fold modifier enzyme 5 (UBA5), E1, Ubiquitin fold modifier 1 (UFM1), Ubiquitin fold modifier conjugating enzyme2 (UFC1), Ufmylation, LIGASE ;; LIGASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.89
Radius of gyration Rg (electron density) rg_electron26.30
Forward intensity I(0) i029367400.00
Molecular weight molecular_weight42691.0 kDa
Excluded volume excluded_volume53931 ų
Envelope volume envelope_volume68503 ų
Hydration-shell volume shell_volume22754 ų
Envelope diameter envelope_diameter93.1
Shell Rg shell_rg32.15
Envelope Rg envelope_rg26.13
Shape Rg shape_rg26.27
Total Rg total_rg27.08
Total atoms total_atoms3000
Residues n_residues354
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax91.2
Rg (real space) rg_real27.04
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real2.9370e+07
I(0) uncertainty (real space) i0_real_error4.9150e+05
Rg (reciprocal space) rg_reciprocal26.99
I(0) (reciprocal space) i0_reciprocal29370000.0000
Solution quality estimate total_estimate0.8453
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7
Skewness Skewness skewness0.410
Kurtosis Kurtosis kurtosis-0.565
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7189000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.738; Smooth: 0.970

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)