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PDBsum entry 2xb2

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protein dna_rna ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2xb2
Jmol PyMol
Contents
Protein chains
390 a.a. *
143 a.a. *
89 a.a. *
15 a.a. *
57 a.a. *
17 a.a. *
DNA/RNA
Ligands
ALA-GLU-ARG
ANP ×2
Metals
_MG ×2
* Residue conservation analysis
PDB id:
2xb2
Name: Hydrolase
Title: Crystal structure of the core mago-y14-eif4aiii-barentsz- upf3b assembly shows how the ejc is bridged to the nmd machinery
Structure: Eukaryotic initiation factor 4a-iii. Chain: a, x. Synonym: eif4aiii, eukaryotic translation initiation factor 4a isoform 3, atp-dependent RNA helicase eif4a-3, atp-dependent RNA helicase ddx48, dead box protein 48, eukaryotic initiation factor 4a-like nuk-34, nuclear matrix protein 265, nmp 265. Engineered: yes. RNA poly-u-ribonucleotide.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes.
Resolution:
3.40Å     R-factor:   0.220     R-free:   0.260
Authors: G.Buchwald,J.Ebert,C.Basquin,J.Sauliere,U.Jayachandran, F.Bono,H.Le Hir,E.Conti
Key ref: G.Buchwald et al. (2010). Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex. Proc Natl Acad Sci U S A, 107, 10050-10055. PubMed id: 20479275
Date:
03-Apr-10     Release date:   12-May-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P38919  (IF4A3_HUMAN) -  Eukaryotic initiation factor 4A-III
Seq:
Struc:
411 a.a.
390 a.a.
Protein chains
Pfam   ArchSchema ?
P61326  (MGN_HUMAN) -  Protein mago nashi homolog
Seq:
Struc:
146 a.a.
143 a.a.
Protein chains
Pfam   ArchSchema ?
Q9Y5S9  (RBM8A_HUMAN) -  RNA-binding protein 8A
Seq:
Struc:
174 a.a.
89 a.a.
Protein chain
Pfam   ArchSchema ?
Q9BZI7  (REN3B_HUMAN) -  Regulator of nonsense transcripts 3B
Seq:
Struc:
483 a.a.
15 a.a.
Protein chains
Pfam   ArchSchema ?
O15234  (CASC3_HUMAN) -  Protein CASC3
Seq:
Struc:
 
Seq:
Struc:
703 a.a.
57 a.a.
Protein chain
Pfam   ArchSchema ?
Q9BZI7  (REN3B_HUMAN) -  Regulator of nonsense transcripts 3B
Seq:
Struc:
483 a.a.
17 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.00% similarity
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     catalytic step 2 spliceosome   12 terms 
  Biological process     exploration behavior   31 terms 
  Biochemical function     selenocysteine insertion sequence binding     13 terms  

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 107:10050-10055 (2010)
PubMed id: 20479275  
 
 
Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.
G.Buchwald, J.Ebert, C.Basquin, J.Sauliere, U.Jayachandran, F.Bono, H.Le Hir, E.Conti.
 
  ABSTRACT  
 
In mammals, Up-frameshift proteins (UPFs) form a surveillance complex that interacts with the exon junction complex (EJC) to elicit nonsense-mediated mRNA decay (NMD). UPF3b is the component of the surveillance complex that bridges the interaction with the EJC. Here, we report the 3.4 A resolution crystal structure of a minimal UPF3b-EJC assembly, consisting of the interacting domains of five proteins (UPF3b, MAGO, Y14, eIF4AIII, and Barentsz) together with RNA and adenylyl-imidodiphosphate. Human UPF3b binds with the C-terminal domain stretched over a composite surface formed by eIF4AIII, MAGO, and Y14. Residues that affect NMD when mutated are found at the core interacting surfaces, whereas differences between UPF3b and UPF3a map at peripheral interacting residues. Comparison with the binding mode of the protein PYM underscores how a common molecular surface of MAGO and Y14 recognizes different proteins acting at different times in the same pathway. The binding mode to eIF4AIII identifies a surface hot spot that is used by different DEAD-box proteins to recruit their regulators.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23211765 O.Mühlemann (2012).
Intimate liaison with SR proteins brings exon junction complexes to unexpected places.
  Nat Struct Mol Biol, 19, 1209-1211.  
22522823 R.Melero, G.Buchwald, R.Castaño, M.Raabe, D.Gil, M.Lázaro, H.Urlaub, E.Conti, and O.Llorca (2012).
The cryo-EM structure of the UPF-EJC complex shows UPF1 poised toward the RNA 3' end.
  Nat Struct Mol Biol, 19, 498.  
23072888 S.Kervestin, and A.Jacobson (2012).
NMD: a multifaceted response to premature translational termination.
  Nat Rev Mol Cell Biol, 13, 700-712.  
21419344 S.Chakrabarti, U.Jayachandran, F.Bonneau, F.Fiorini, C.Basquin, S.Domcke, H.Le Hir, and E.Conti (2011).
Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2.
  Mol Cell, 41, 693-703.
PDB codes: 2xzl 2xzo 2xzp
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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