9EN7 | pdb_00009en7

Hrp48 RRM1 domain

• PDB DOI: https://doi.org/10.2210/pdb9EN7/pdb

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


• Deposited: 2024-03-12 Released: 2024-11-13 
• Deposition Author(s): Lomoschitz, A., Hennig, J., Murciano, B., Meyer, J.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.170 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

The Drosophila RNA binding protein Hrp48 binds a specific RNA sequence of the msl-2 mRNA 3' UTR to regulate translation.

Lomoschitz, A., Meyer, J., Guitart, T., Krepl, M., Lapouge, K., Hayn, C., Schweimer, K., Simon, B., Sponer, J., Gebauer, F., Hennig, J.

(2024) Biophys Chem 316: 107346-107346

• PubMed: 39504588 
• DOI: https://doi.org/10.1016/j.bpc.2024.107346
• Primary Citation of Related Structures:  
  9EN7


• PubMed Abstract: 
  

  Repression of msl-2 mRNA translation is essential for viability of Drosophila melanogaster females to prevent hypertranscription of both X chromosomes. This translational control event is coordinated by the female-specific protein Sex-lethal (Sxl) which recruits the RNA binding proteins Unr and Hrp48 to the 3' untranslated region (UTR) of the msl-2 transcript and represses translation initiation. The mechanism exerted by Hrp48 during translation repression and its interaction with msl-2 are not well understood. Here we investigate the RNA binding specificity and affinity of the tandem RNA recognition motifs of Hrp48. Using NMR spectroscopy, molecular dynamics simulations and isothermal titration calorimetry, we identified the exact region of msl-2 3' UTR recognized by Hrp48. Additional biophysical experiments and translation assays give further insights into complex formation of Hrp48, Unr, Sxl and RNA. Our results show that Hrp48 binds independent of Sxl and Unr downstream of the E and F binding sites of Sxl and Unr to msl-2.

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Organizational Affiliation: 
• Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Department of Biochemistry IV - Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany.
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain.
Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic.
Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany.
Department of Biochemistry IV - Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany.
Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Molecular Biology and Biophysics - University of Connecticut Health Center, Farmington, CT 06030, USA.
Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc 783 71, Czech Republic.
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Department of Biochemistry IV - Biophysical Chemistry, University of Bayreuth, 95447 Bayreuth, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.29 kDa 
• Atom Count: 803 
• Modeled Residue Count: 84 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterogeneous nuclear ribonucleoprotein 27C	A	90	Drosophila melanogaster	Mutation(s): 0  Gene Names: Hrb27C, hrp48, Rbp7, CG10377
UniProt
Find proteins for P48809 (Drosophila melanogaster) Explore P48809  Go to UniProtKB:  P48809

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.170 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.344	α = 90
b = 45.496	β = 90
c = 57.026	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Lomoschitz, A., Hennig, J., Murciano, B., Meyer, J.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	HE 7291/5-1

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Database references