2HXY | pdb_00002hxy

Crystal structure of human apo-eIF4AIII

• PDB DOI: https://doi.org/10.2210/pdb2HXY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-04 Released: 2006-08-15 
• Deposition Author(s): Johansen, J.S., Andersen, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.308 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.275 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Literature

Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA.

Andersen, C.B., Ballut, L., Johansen, J.S., Chamieh, H., Nielsen, K.H., Oliveira, C.L., Pedersen, J.S., Seraphin, B., Le Hir, H., Andersen, G.R.

(2006) Science 313: 1968-1972

• PubMed: 16931718 
• DOI: https://doi.org/10.1126/science.1131981
• Primary Citation Related Structures: 
  2HXY, 2HYI


• PubMed Abstract: 
  

  In higher eukaryotes, a multiprotein exon junction complex is deposited on spliced messenger RNAs. The complex is organized around a stable core, which serves as a binding platform for numerous factors that influence messenger RNA function. Here, we present the crystal structure of a tetrameric exon junction core complex containing the DEAD-box adenosine triphosphatase (ATPase) eukaryotic initiation factor 4AIII (eIF4AIII) bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic. eIF4AIII interacts with the phosphate-ribose backbone of six consecutive nucleotides and prevents part of the bound RNA from being double stranded. The MAGOH and Y14 subunits lock eIF4AIII in a prehydrolysis state, and activation of the ATPase probably requires only modest conformational changes in eIF4AIII motif I.

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Organizational Affiliation: 
• Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 179.27 kDa 
• Atom Count: 12,080 
• Modeled Residue Count: 1,504 
• Deposited Residue Count: 1,564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX48	A, B, C, D	391	Homo sapiens	Mutation(s): 0  Gene Names: DDX48, EIF4A3, KIAA0111 EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P38919 (Homo sapiens) Explore P38919  Go to UniProtKB:  P38919
PHAROS:  P38919 GTEx:  ENSG00000141543

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.308 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.275 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.22	α = 90
b = 238.05	β = 90
c = 79.52	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): Johansen, J.S., Andersen, G.R.

Revision History  

• Version 1.0: 2006-08-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references