6DCL

Crystal structure of UP1 bound to pri-miRNA-18a terminal loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.497 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1.

Kooshapur, H.Choudhury, N.R.Simon, B.Muhlbauer, M.Jussupow, A.Fernandez, N.Jones, A.N.Dallmann, A.Gabel, F.Camilloni, C.Michlewski, G.Caceres, J.F.Sattler, M.

(2018) Nat Commun 9: 2479-2479

  • DOI: 10.1038/s41467-018-04871-9

  • PubMed Abstract: 
  • Post-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. Recognition of the terminal loop of precursor miRNAs by RNA-binding proteins (RBPs) influences their processing; however, the mechanistic basis for ...

    Post-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. Recognition of the terminal loop of precursor miRNAs by RNA-binding proteins (RBPs) influences their processing; however, the mechanistic basis for how levels of individual or subsets of miRNAs are regulated is mostly unexplored. We previously showed that hnRNP A1, an RBP implicated in many aspects of RNA processing, acts as an auxiliary factor that promotes the Microprocessor-mediated processing of pri-mir-18a. Here, by using an integrative structural biology approach, we show that hnRNP A1 forms a 1:1 complex with pri-mir-18a where both RNA recognition motifs (RRMs) bind to cognate RNA sequence motifs in the terminal loop of pri-mir-18a. Terminal loop binding induces an allosteric destabilization of base-pairing in the pri-mir-18a stem that promotes its downstream processing. Our results highlight terminal loop RNA recognition by RBPs as a potential general principle of miRNA biogenesis and regulation.


    Organizational Affiliation

    Institute of Structural Biology, Helmholtz Zentrum M√ľnchen, Neuherberg, 85764, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heterogeneous nuclear ribonucleoprotein A1
A, B
191Homo sapiensMutation(s): 0 
Gene Names: HNRNPA1 (HNRPA1)
Find proteins for P09651 (Homo sapiens)
Go to Gene View: HNRNPA1
Go to UniProtKB:  P09651
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*UP*AP*GP*AP*UP*UP*AP*GP*C)-3')C,D12Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 127.028α = 90.00
b = 127.028β = 90.00
c = 147.064γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1035
German Research FoundationGermanyGRK1721

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references