› 2xb2

X-ray diffraction
3.4Å resolution

Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery

Released:
DOI: 10.2210/pdb2xb2/pdb
PDB entry 2xb2 coloured by chain, front view.
PDB entry 2xb2 coloured by chain, side view.
PDB entry 2xb2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.
Buchwald G, Ebert J, Basquin C, Sauliere J, Jayachandran U, Bono F, Le Hir H, Conti E
Proc Natl Acad Sci U S A 107 10050-5 (2010)
PMID: 20479275

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero hexamer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-219119 (preferred)
Entry contents:
6 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (7 distinct):
Eukaryotic initiation factor 4A-III Chains: A, X
Molecule details ›
Chains: A, X
Length: 411 amino acids
Theoretical weight: 46.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38919 (Residues: 1-411; Coverage: 100%)
Gene names: DDX48, EIF4A3, KIAA0111
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Protein mago nashi homolog Chains: C, Y
Molecule details ›
Chains: C, Y
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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: D, Z
Molecule details ›
Chains: D, Z
Length: 90 amino acids
Theoretical weight: 10.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y5S9 (Residues: 66-155; Coverage: 52%)
Gene names: HSPC114, MDS014, RBM8, RBM8A
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
Regulator of nonsense transcripts 3B Chain: F
Molecule details ›
Chain: F
Length: 3 amino acids
Theoretical weight: 375 Da
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BZI7 (Residues: 466-468; Coverage: 1%)
Gene names: RENT3B, UPF3B, UPF3X
Regulator of nonsense transcripts 3B Chains: G, U
Molecule details ›
Chains: G, U
Length: 60 amino acids
Theoretical weight: 6.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BZI7 (Residues: 424-483; Coverage: 12%)
Gene names: RENT3B, UPF3B, UPF3X
Protein CASC3 Chains: S, T
Molecule details ›
Chains: S, T
Length: 150 amino acids
Theoretical weight: 17.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O15234 (Residues: 137-286; Coverage: 21%)
Gene names: CASC3, MLN51
Sequence domains: CASC3/Barentsz eIF4AIII binding
RNA POLY-U-RIBONUCLEOTIDE Chains: E, R
Molecule details ›
Chains: E, R
Length: 15 nucleotides
Theoretical weight: 4.55 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ANP 2 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P41212
Unit cell:
a: 134.8Å b: 134.8Å c: 227.25Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.26
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

32 review citations

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

8 mentions without citation

Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics.
Pawlicka et al. (2020)
7 more