Crystal structure of the RRM domain of SYNCRIP

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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This is version 1.2 of the entry. See complete history


SYNCRIP, a new player in pri-let-7a processing.

Chen, Y.Chan, J.Chen, W.Li, J.Sun, M.Kannan, G.S.Mok, Y.K.Yuan, Y.A.Jobichen, C.

(2020) RNA 26: 290-305

  • DOI: https://doi.org/10.1261/rna.072959.119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    microRNAs (miRNAs), a class of small and endogenous molecules that control gene expression, are broadly involved in biological processes. Although a number of cofactors that assist or antagonize let-7 miRNA biogenesis are well-established, more auxiliary factors remain to be investigated. Here, we identified SYNCRIP (Synaptotagmin Binding Cytoplasmic RNA Interacting Protein) as a new player for let-7a miRNA. SYNCRIP interacts with pri-let-7a both in vivo and in vitro. Knockdown of SYNCRIP impairs, while overexpression of SYNCRIP promotes, the expression of let-7a miRNA. A broad miRNA profiling analysis revealed that silencing of SYNCRIP regulates the expression of a set of mature miRNAs positively or negatively. In addition, SYNCRIP is associated with microprocessor complex and promotes the processing of pri-let-7a. Strikingly, the terminal loop of pri-let-7a was shown to be the main contributor for its interaction with SYNCRIP. Functional studies demonstrated that the SYNCRIP RRM2-3 domain can promote the processing of pri-let-7a. Structure-based alignment of RRM2-3 with other RNA binding proteins identified the residues likely to participate in protein-RNA interactions. Taken together, these findings suggest the promising role that SYNCRIP plays in miRNA regulation, thus providing insights into the function of SYNCRIP in eukaryotic development.

  • Organizational Affiliation

    Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heterogeneous nuclear ribonucleoprotein Q193Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60506 (Homo sapiens)
Explore O60506 
Go to UniProtKB:  O60506
PHAROS:  O60506
GTEx:  ENSG00000135316 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60506
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.634α = 90
b = 103.634β = 90
c = 49.289γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description