1lj2

Recognition of eIF4G by Rotavirus NSP3 reveals a basis for mRNA circularization

Method: X-RAY DIFFRACTION Dmax: 100.3 Å Quality: REASONABLE

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

NONSTRUCTURAL RNA-BINDING PROTEIN 34

Simian rotavirus A/SA11

UniProt P03536

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 206–315 Chain B; UniProt 206–315 Fragment:C-terminal domain Mutation:C306S C314S eukaryotic protein synthesis initiation factor × 2 (Q04637) AU GOLD ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;275 K;PEG-MME 550, glucose, theophylline, unbuffered, VAPOR DIFFUSION, HANGING DROP at 275K Resolution 2.38 Å R-free 0.272

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.

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

View Construct and Data Evidence
UniProt name VN34_ROTS1
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–110; UniProt 206–315 Author chain B; PDBConstruct 1–110; UniProt 206–315

eukaryotic protein synthesis initiation factor

OrganismNot specified

UniProt Q04637

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 172–199 Chain D; UniProt 172–199 Fragment:residues 132-159 of AAC82471 NONSTRUCTURAL RNA-BINDING PROTEIN 34 × 2 (P03536) AU GOLD ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;275 K;PEG-MME 550, glucose, theophylline, unbuffered, VAPOR DIFFUSION, HANGING DROP at 275K Resolution 2.38 Å R-free 0.272

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.

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

View Construct and Data Evidence
UniProt name IF4G1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–28; UniProt 172–199 Author chain D; PDBConstruct 1–28; UniProt 172–199

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 1lj2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1lj2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1lj2
Deposition date deposition_date2002-04-18
Structure title titleRecognition of eIF4G by Rotavirus NSP3 reveals a basis for mRNA circularization
Keywords keywordsNSP3; homodimer; eIF4G; Rotavirus; translation; mRNA; closed loop; coiled coil, Viral protein- translation COMPLEX; Viral protein/ translation
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.38
Radius of gyration Rg (electron density) rg_electron26.01
Forward intensity I(0) i018045800.00
Molecular weight molecular_weight30801.0 kDa
Excluded volume excluded_volume37733 ų
Envelope volume envelope_volume47979 ų
Hydration-shell volume shell_volume18395 ų
Envelope diameter envelope_diameter99.8
Shell Rg shell_rg28.19
Envelope Rg envelope_rg27.13
Shape Rg shape_rg25.81
Total Rg total_rg26.85
Total atoms total_atoms2131
Residues n_residues265
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 dmax100.3
Rg (real space) rg_real27.03
Rg uncertainty (real space) rg_real_error1.10
I(0) (real space) i0_real1.8050e+07
I(0) uncertainty (real space) i0_real_error2.9830e+05
Rg (reciprocal space) rg_reciprocal26.83
I(0) (reciprocal space) i0_reciprocal18040000.0000
Solution quality estimate total_estimate0.7021
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary23.4
Skewness Skewness skewness0.874
Kurtosis Kurtosis kurtosis0.290
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1954000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.347; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.193; Smooth: 0.890

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1lj2a_
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.13 — Rotavirus nonstructural proteins
Family Family familyh.1.13.2 — NSP3 C-terminal domain, NS34
Domain ID domain_idd1lj2b_
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.13 — Rotavirus nonstructural proteins
Family Family familyh.1.13.2 — NSP3 C-terminal domain, NS34

CATH v4.4 (2 domains)

Domain ID domain_id1lj2A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily970 — Nonstructural RNA-binding protein
Domain ID domain_id1lj2B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily970 — Nonstructural RNA-binding protein

8. Citations (1)

9. Files and Curves (10)