6S8R | pdb_00006s8r

D. melanogaster RNA helicase Me31B in complex with GIGYF

• PDB DOI: https://doi.org/10.2210/pdb6S8R/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-10 Released: 2019-09-04 
• Deposition Author(s): Peter, D., Valkov, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression.

Peter, D., Ruscica, V., Bawankar, P., Weber, R., Helms, S., Valkov, E., Igreja, C., Izaurralde, E.

(2019) Genes Dev 33: 1355-1360

• PubMed: 31439631 
• DOI: https://doi.org/10.1101/gad.329219.119
• Primary Citation Related Structures: 
  6S8R, 6S8S


• PubMed Abstract: 
  

  GIGYF (Grb10-interacting GYF [glycine-tyrosine-phenylalanine domain]) proteins coordinate with 4EHP (eIF4E [eukaryotic initiation factor 4E] homologous protein), the DEAD (Asp-Glu-Ala-Asp)-box helicase Me31B/DDX6, and mRNA-binding proteins to elicit transcript-specific repression. However, the underlying molecular mechanism remains unclear. Here, we report that GIGYF contains a motif necessary and sufficient for direct interaction with Me31B/DDX6. A 2.4 Å crystal structure of the GIGYF-Me31B complex reveals that this motif arranges into a coil connected to a β hairpin on binding to conserved hydrophobic patches on the Me31B RecA2 domain. Structure-guided mutants indicate that 4EHP-GIGYF-DDX6 complex assembly is required for tristetraprolin-mediated down-regulation of an AU-rich mRNA, thus revealing the molecular principles of translational repression.

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Organizational Affiliation: 
• Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.
European Molecular Biology Laboratory, 38042 Grenoble Cedex 9, France.
Institute of Molecular Biology, 55128 Mainz, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content 

• Total Structure Weight: 23.09 kDa 
• Atom Count: 1,621 
• Modeled Residue Count: 194 
• Deposited Residue Count: 199 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase me31b	A	172	Drosophila melanogaster	Mutation(s): 0  Gene Names: me31B, CG4916 EC: 3.6.4.13
UniProt
Find proteins for P23128 (Drosophila melanogaster) Explore P23128  Go to UniProtKB:  P23128

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GIGYF family protein CG11148	B	27	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG11148
UniProt
Find proteins for Q7KQM6 (Drosophila melanogaster) Explore Q7KQM6  Go to UniProtKB:  Q7KQM6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A], E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.44	α = 90
b = 41.96	β = 90
c = 122.67	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Peter, D., Valkov, E.

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary