› 3ex7

X-ray diffraction
2.3Å resolution

The crystal structure of EJC in its transition state

Released:
DOI: 10.2210/pdb3ex7/pdb
PDB entry 3ex7 coloured by chain, front view.
PDB entry 3ex7 coloured by chain, side view.
PDB entry 3ex7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of ATP turnover inhibition in the EJC.
Nielsen KH, Chamieh H, Andersen CB, Fredslund F, Hamborg K, Le Hir H, Andersen GR
RNA 15 67-75 (2009)
PMID: 19033377

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127369 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (5 distinct):
Protein mago nashi homolog Chains: A, E
Molecule details ›
Chains: A, E
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61326 (Residues: 1-146; Coverage: 100%)
Gene names: MAGOH, MAGOHA
Sequence domains: Mago nashi protein
Structure domains: Mago nashi
RNA-binding protein 8A Chains: B, G
Molecule details ›
Chains: B, G
Length: 126 amino acids
Theoretical weight: 14.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y5S9 (Residues: 51-174; Coverage: 71%)
Gene names: HSPC114, MDS014, RBM8, RBM8A
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
Eukaryotic initiation factor 4A-III Chains: C, H
Molecule details ›
Chains: C, H
Length: 413 amino acids
Theoretical weight: 47.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P38919 (Residues: 1-411; Coverage: 100%)
Gene names: DDX48, EIF4A3, KIAA0111
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Protein CASC3 Chains: D, I
Molecule details ›
Chains: D, I
Length: 146 amino acids
Theoretical weight: 17.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O15234 (Residues: 138-283; Coverage: 21%)
Gene names: CASC3, MLN51
Sequence domains: CASC3/Barentsz eIF4AIII binding
RNA (5'-R(*UP*UP*UP*UP*UP*U)-3') Chains: F, J
Molecule details ›
Chains: F, J
Length: 6 nucleotides
Theoretical weight: 1.79 KDa

Ligands and Environments

3 bound ligands:
Ligand ADP 2 x ADP
Ligand AF3 2 x AF3
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 182.04Å b: 100.75Å c: 145.88Å
α: 90° β: 112.08° γ: 90°
R-values:
R R work R free
0.207 0.206 0.251
Expression system: Escherichia coli

Quick links

Citations

26 review citations

From unwinding to clamping - the DEAD box RNA helicase family.
Linder et al. (2011)
25 more

9 mentions without citation

Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins.
Squeglia et al. (2020)
8 more