6FPX

Structure of S. pombe Mmi1 in complex with 11-mer RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding.

Stowell, J.A.W., Wagstaff, J.L., Hill, C.H., Yu, M., McLaughlin, S.H., Freund, S.M.V., Passmore, L.A.

(2018) J Biol Chem 293: 9210-9222

  • DOI: https://doi.org/10.1074/jbc.RA118.002291
  • Primary Citation of Related Structures:  
    6FPP, 6FPQ, 6FPX

  • PubMed Abstract: 

    • Mmi1 is an essential RNA-binding protein in the fission yeast Schizosaccharomyces pombe that eliminates meiotic transcripts during normal vegetative growth. Mmi1 contains a YTH domain that binds specific RNA sequences, targeting mRNAs for degradation ...

    Mmi1 is an essential RNA-binding protein in the fission yeast Schizosaccharomyces pombe that eliminates meiotic transcripts during normal vegetative growth. Mmi1 contains a YTH domain that binds specific RNA sequences, targeting mRNAs for degradation. The YTH domain of Mmi1 uses a noncanonical RNA-binding surface that includes contacts outside the conserved fold. Here, we report that an N-terminal extension that is proximal to the YTH domain enhances RNA binding. Using X-ray crystallography, NMR, and biophysical methods, we show that this low-complexity region becomes more ordered upon RNA binding. This enhances the affinity of the interaction of the Mmi1 YTH domain with specific RNAs by reducing the dissociation rate of the Mmi1-RNA complex. We propose that the low-complexity region influences RNA binding indirectly by reducing dynamic motions of the RNA-binding groove and stabilizing a conformation of the YTH domain that binds to RNA with high affinity. Taken together, our work reveals how a low-complexity region proximal to a conserved folded domain can adopt an ordered structure to aid nucleic acid binding.

    Organizational Affiliation: 

    From the MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom passmore@mrc-lmb.cam.ac.uk.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YTH domain-containing protein mmi1A, C, E192Schizosaccharomyces pombeMutation(s): 0 
Gene Names: mmi1, SPCC736.12c
UniProt
Find proteins for O74958 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74958 
Go to UniProtKB:  O74958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74958
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*UP*AP*AP*AP*CP*CP*UP*A)-3')B, D, F11Schizosaccharomyces pombe
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth C],
I [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.331α = 90
b = 105.331β = 90
c = 66.706γ = 120
Software Package:
Software NamePurpose
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105192715
European Research Council261151

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references