4ujd

mammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state

Method: ELECTRON MICROSCOPY Dmax: 247.8 Å Quality: EXCELLENT

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

EIF5B

OrganismNot specified

UniProt G1TRL5

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–RNA Heteromer Protein × 77 RNA 6 PDB declaration: 83-meric(83) Consistent with all polymer counts Chain BB; UniProt 583–1209 Not recorded 28S Ribosomal RNA × 1 5.8S Ribosomal RNA × 1 5S Ribosomal RNA × 1 60S RIBOSOMAL PROTEIN L8 × 1 60S RIBOSOMAL PROTEIN L3 × 1 60S RIBOSOMAL PROTEIN L4 × 1 60S RIBOSOMAL PROTEIN L5 × 1 60S RIBOSOMAL PROTEIN L6 × 1 60S RIBOSOMAL PROTEIN L7 × 1 60S RIBOSOMAL PROTEIN L7A × 1 60S RIBOSOMAL PROTEIN L9 × 1 60S RIBOSOMAL PROTEIN L10 × 1 60S RIBOSOMAL PROTEIN L11 × 1 60S RIBOSOMAL PROTEIN L13 × 1 60S RIBOSOMAL PROTEIN L14 × 1 60S RIBOSOMAL PROTEIN L15 × 1 60S RIBOSOMAL PROTEIN L13A × 1 60S RIBOSOMAL PROTEIN L17 × 1 60S RIBOSOMAL PROTEIN L18 × 1 60S RIBOSOMAL PROTEIN L19 × 1 60S RIBOSOMAL PROTEIN L18A × 1 60S RIBOSOMAL PROTEIN L21 × 1 60S RIBOSOMAL PROTEIN L22 × 1 60S RIBOSOMAL PROTEIN L23 × 1 60S RIBOSOMAL PROTEIN L24 × 1 60S RIBOSOMAL PROTEIN L23A × 1 60S RIBOSOMAL PROTEIN L26 × 1 60S RIBOSOMAL PROTEIN L27 × 1 60S RIBOSOMAL PROTEIN L27A × 1 60S RIBOSOMAL PROTEIN L29 × 1 60S RIBOSOMAL PROTEIN L30 × 1 60S RIBOSOMAL PROTEIN L31 × 1 60S RIBOSOMAL PROTEIN L32 × 1 60S RIBOSOMAL PROTEIN L35A × 1 60S RIBOSOMAL PROTEIN L34 × 1 60S RIBOSOMAL PROTEIN L35 × 1 60S RIBOSOMAL PROTEIN L36 × 1 60S RIBOSOMAL PROTEIN L37 × 1 60S RIBOSOMAL PROTEIN L38 × 1 60S RIBOSOMAL PROTEIN L39 × 1 UBIQUITIN-60S RIBOSOMAL PROTEIN L40 × 1 60S RIBOSOMAL PROTEIN L41 × 1 60S RIBOSOMAL PROTEIN L36A × 1 60S RIBOSOMAL PROTEIN L37A × 1 60S RIBOSOMAL PROTEIN L28 × 1 60S RIBOSOMAL PROTEIN L10A × 1 TRNA × 1 HCV-IRES × 1 18S Ribosomal RNA × 1 40S RIBOSOMAL PROTEIN US2 × 1 40S RIBOSOMAL PROTEIN ES1 × 1 40S RIBOSOMAL PROTEIN US5 × 1 40S RIBOSOMAL PROTEIN US3 × 1 40S RIBOSOMAL PROTEIN ES4 × 1 40S RIBOSOMAL PROTEIN US7 × 1 40S RIBOSOMAL PROTEIN ES6 × 1 40S RIBOSOMAL PROTEIN ES7 × 1 40S RIBOSOMAL PROTEIN ES8 × 1 40S RIBOSOMAL PROTEIN US4 × 1 40S RIBOSOMAL PROTEIN ES10 × 1 40S RIBOSOMAL PROTEIN US17 × 1 40S RIBOSOMAL PROTEIN ES12 × 1 40S RIBOSOMAL PROTEIN ES15 × 1 40S RIBOSOMAL PROTEIN ES11 × 1 40S RIBOSOMAL PROTEIN US19 × 1 40S RIBOSOMAL PROTEIN US9 × 1 40S RIBOSOMAL PROTEIN ES17 × 1 40S RIBOSOMAL PROTEIN US13 × 1 40S RIBOSOMAL PROTEIN ES19 × 1 40S RIBOSOMAL PROTEIN US10 × 1 40S RIBOSOMAL PROTEIN ES21 × 1 40S RIBOSOMAL PROTEIN US8 × 1 40S RIBOSOMAL PROTEIN US12 × 1 40S RIBOSOMAL PROTEIN ES24 × 1 40S RIBOSOMAL PROTEIN ES25 × 1 40S RIBOSOMAL PROTEIN ES26 × 1 40S RIBOSOMAL PROTEIN ES27 × 1 40S RIBOSOMAL PROTEIN ES28 × 1 40S RIBOSOMAL PROTEIN US14 × 1 40S RIBOSOMAL PROTEIN ES30 × 1 40S RIBOSOMAL PROTEIN ES31 × 1 40S RIBOSOMAL PROTEIN RACK1 × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT;pH 7.6;20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT cryo-EM vitrification conditions:Cryogen ETHANE;VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING, Resolution 8.90 Å

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.

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

View Construct and Data Evidence
UniProt name G1TRL5_RABIT
Isoform
PDB entities 48
Chains and sequence ranges Author chain BB; PDBConstruct 1–627; UniProt 583–1209

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 4ujd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ujd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ujd
Deposition date deposition_date2014-06-18
Structure title titlemammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state
Keywords keywordsRIBOSOME, TRANSLATION INITIATION, HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE, EUKARYOTIC INITIATION FACTOR 5B; RIBOSOME
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier96.36
Radius of gyration Rg (electron density) rg_electron96.93
Forward intensity I(0) i0312568000000.00
Molecular weight molecular_weight3305700.0 kDa
Excluded volume excluded_volume3531100 ų
Envelope volume envelope_volume6187700 ų
Hydration-shell volume shell_volume481880 ų
Envelope diameter envelope_diameter316.9
Shell Rg shell_rg114.20
Envelope Rg envelope_rg95.69
Shape Rg shape_rg96.97
Total Rg total_rg96.89
Total atoms total_atoms223911
Residues n_residues17928
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 dmax247.8
Rg (real space) rg_real93.75
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real2.9930e+11
I(0) uncertainty (real space) i0_real_error4.8590e+09
Rg (reciprocal space) rg_reciprocal98.39
I(0) (reciprocal space) i0_reciprocal314700000000.0000
Solution quality estimate total_estimate0.9106
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary108.4
Skewness Skewness skewness0.097
Kurtosis Kurtosis kurtosis-0.607
Angular range angular_range— – 0.0800 −1
Current regularization parameter α current_alpha0.9805
Highest regularization parameter α highest_alpha20660000000.0000
Real-space data points n_real_points17
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 0.949; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (85)

8. Citations (1)

9. Files and Curves (10)