3jui

Crystal Structure of the C-terminal Domain of Human Translation Initiation Factor eIF2B epsilon Subunit

Method: X-RAY DIFFRACTION Dmax: 57.3 Å Quality: GOOD

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

Translation initiation factor eIF-2B subunit epsilon

Homo sapiens

UniProt Q13144

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 548–721 Fragment:C-terminal Domain Mutation:E678G Non-standard monomer:Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.7;289 K;PEG8000, Calcium acetate, Sodium Cocadylate, pH 7.7, vapor diffusion, temperature 289K Resolution 2.00 Å R-free 0.279

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.

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EI2BE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 9–182; UniProt 548–721

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 3jui

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3jui
Deposition date deposition_date2009-09-15
Structure title titleCrystal Structure of the C-terminal Domain of Human Translation Initiation Factor eIF2B epsilon Subunit
Keywords keywords;HEAT repeat, guanine nucleotide exchange factor, translation initiation factor, Disease mutation, Initiation factor, Leukodystrophy, Phosphoprotein, Protein biosynthesis, TRANSLATION ;; TRANSLATION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.93
Radius of gyration Rg (electron density) rg_electron16.40
Forward intensity I(0) i07860030.00
Molecular weight molecular_weight20495.0 kDa
Excluded volume excluded_volume25565 ų
Envelope volume envelope_volume29551 ų
Hydration-shell volume shell_volume15296 ų
Envelope diameter envelope_diameter58.9
Shell Rg shell_rg22.24
Envelope Rg envelope_rg16.73
Shape Rg shape_rg16.43
Total Rg total_rg17.32
Total atoms total_atoms1428
Residues n_residues169
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 dmax57.3
Rg (real space) rg_real17.82
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real7.8600e+06
I(0) uncertainty (real space) i0_real_error9.2260e+04
Rg (reciprocal space) rg_reciprocal17.83
I(0) (reciprocal space) i0_reciprocal7860000.0000
Solution quality estimate total_estimate0.8130
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.2
Skewness Skewness skewness0.137
Kurtosis Kurtosis kurtosis-0.389
Angular range angular_range— – 0.4450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1183000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3juia1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.0 — automated matches
Domain ID domain_idd3juia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id3juiA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily180

8. Citations (1)

9. Files and Curves (10)