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5k4d

Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 3

Method: X-RAY DIFFRACTION Dmax: 101.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Eukaryotic translation initiation factor 3 subunit D

Nasonia vitripennis

UniProt K7IM66

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 172–537 Fragment：unp residues 172-537 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；200 mM NaCl, 100 mM Tris 8.5, 25% PEG-3350 Resolution 2.00 Å R-free 0.208
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 172–537 Fragment：unp residues 172-537 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；200 mM NaCl, 100 mM Tris 8.5, 25% PEG-3350 Resolution 2.00 Å R-free 0.208

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 5K4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5K4B Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 1 Deposited 2016-05-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 172–537（366 aa） Fragment：unp residues 172-537
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；200 mM (NH4)2SO4, 100 mM Bis-Tris 6.5, 23-27% PEG-3350
Resolution 1.40 Å R-free 0.193
5K4B Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 1 Deposited 2016-05-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 172–537（366 aa） Fragment：unp residues 172-537
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；200 mM (NH4)2SO4, 100 mM Bis-Tris 6.5, 23-27% PEG-3350
Resolution 1.40 Å R-free 0.193
5K4C Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 2 Deposited 2016-05-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 172–537（366 aa） Fragment：unp residues 172-537
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.6-1.8 M Ammonium Citrate pH 7.0
Resolution 1.70 Å R-free 0.196
6W2T Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) Deposited 2020-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 44-meric
Chain 9 1–558（558 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2.5s and flash cooled in liquid ethane
Resolution 3.36 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K7IM66_NASVI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–368； UniProt 172–537 Author chain B； PDBConstruct 3–368； UniProt 172–537

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 5k4d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5k4d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5k4d
Deposition date deposition_date2016-05-20
Structure title titleStructure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 3
Keywords keywordsEukaryotic translation initiation factor 3, cap-binding domain, TRANSLATION; TRANSLATION
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_guinier31.09 Å
Radius of gyration Rg (electron density) rg_electron30.60 Å
Forward intensity I(0) i0106403000.00
Molecular weight molecular_weight80881.0 kDa
Excluded volume excluded_volume100910 ų
Envelope volume envelope_volume125230 ų
Hydration-shell volume shell_volume35168 ų
Envelope diameter envelope_diameter105.5 Å
Shell Rg shell_rg36.59 Å
Envelope Rg envelope_rg30.72 Å
Shape Rg shape_rg30.61 Å
Total Rg total_rg31.05 Å
Total atoms total_atoms5686
Residues n_residues705
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 dmax101.8 Å
Rg (real space) rg_real31.25 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real1.0640e+08
I(0) uncertainty (real space) i0_real_error1.8390e+06
Rg (reciprocal space) rg_reciprocal31.19 Å
I(0) (reciprocal space) i0_reciprocal106400000.0000
Solution quality estimate total_estimate0.8640
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.9 Å
Skewness Skewness skewness0.458
Kurtosis Kurtosis kurtosis-0.446
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35670000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.821
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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)