7NYQ | pdb_00007nyq

Crystal structure of the Mei-P26 NHL domain

• PDB DOI: https://doi.org/10.2210/pdb7NYQ/pdb

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


• Deposited: 2021-03-23 Released: 2022-05-04 
• Deposition Author(s): Salerno-Kochan, A., Gaik, M., Medenbach, J., Glatt, S.
• Funding Organization(s): Polish National Science Centre, Foundation for Polish Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26.

Salerno-Kochan, A., Horn, A., Ghosh, P., Nithin, C., Koscielniak, A., Meindl, A., Strauss, D., Krutyholowa, R., Rossbach, O., Bujnicki, J.M., Gaik, M., Medenbach, J., Glatt, S.

(2022) Life Sci Alliance 5

• PubMed: 35512835 
• DOI: https://doi.org/10.26508/lsa.202201418
• Primary Citation of Related Structures:  
  7NYQ


• PubMed Abstract: 
  

  The TRIM-NHL protein Meiotic P26 (Mei-P26) acts as a regulator of cell fate in Drosophila Its activity is critical for ovarian germline stem cell maintenance, differentiation of oocytes, and spermatogenesis. Mei-P26 functions as a post-transcriptional regulator of gene expression; however, the molecular details of how its NHL domain selectively recognizes and regulates its mRNA targets have remained elusive. Here, we present the crystal structure of the Mei-P26 NHL domain at 1.6 Å resolution and identify key amino acids that confer substrate specificity and distinguish Mei-P26 from closely related TRIM-NHL proteins. Furthermore, we identify mRNA targets of Mei-P26 in cultured Drosophila cells and show that Mei-P26 can act as either a repressor or activator of gene expression on different RNA targets. Our work reveals the molecular basis of RNA recognition by Mei-P26 and the fundamental functional differences between otherwise very similar TRIM-NHL proteins.

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Organizational Affiliation: 
• Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
Postgraduate School of Molecular Medicine, Warsaw, Poland.
Biochemistry I, University of Regensburg, Regensburg, Germany.
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland.
Institute of Biochemistry, University of Giessen, Giessen, Germany.
Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland [e-mail].
Biochemistry I, University of Regensburg, Regensburg, Germany [e-mail].
Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.59 kDa 
• Atom Count: 4,667 
• Modeled Residue Count: 549 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiotic P26, isoform C	A, B	301	Drosophila melanogaster	Mutation(s): 0  Gene Names: mei-P26, AF145661, BcDNA:GH10646, Dmel\CG12218, MEI-P26, meiP26, CG12218, Dmel_CG12218
UniProt
Find proteins for M9PH32 (Drosophila melanogaster) Explore M9PH32  Go to UniProtKB:  M9PH32

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.71	α = 90
b = 116.5	β = 96.36
c = 64.7	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Salerno-Kochan, A., Gaik, M., Medenbach, J., Glatt, S.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2015/19/P/NZ1/02514
Polish National Science Centre	Poland	2019/32/T/NZ1/00420
Foundation for Polish Science	Poland	TECH CORE FACILITY/2017-4/6

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-05-18
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary