7EB1

Solution NMR structure of the RRM domain of RNA binding protein RBM3 from homo sapiens


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition.

Roy, S.Boral, S.Maiti, S.Kushwaha, T.Basak, A.J.Lee, W.Basak, A.Gholap, S.L.Inampudi, K.K.De, S.

(2022) FEBS J 289: 2847-2864

  • DOI: https://doi.org/10.1111/febs.16301
  • Primary Citation of Related Structures:  
    7EB1

  • PubMed Abstract: 

    Human RNA-binding motif 3 protein (RBM3) is a cold-shock protein which functions in various aspects of global protein synthesis, cell proliferation and apoptosis by interacting with the components of basal translational machinery. RBM3 plays important roles in tumour progression and cancer metastasis, and also has been shown to be involved in neuroprotection and endoplasmic reticulum stress response. Here, we have solved the solution NMR structure of the N-terminal 84 residue RNA recognition motif (RRM) of RBM3. The remaining residues are rich in RGG and YGG motifs and are disordered. The RRM domain adopts a βαββαβ topology, which is found in many RNA-binding proteins. NMR-monitored titration experiments and molecular dynamic simulations show that the beta-sheet and two loops form the RNA-binding interface. Hydrogen bond, pi-pi and pi-cation are the key interactions between the RNA and the RRM domain. NMR, size exclusion chromatography and chemical cross-linking experiments show that RBM3 forms oligomers in solution, which is favoured by decrease in temperature, thus, potentially linking it to its function as a cold-shock protein. Temperature-dependent NMR studies revealed that oligomerization of the RRM domain occurs via nonspecific interactions. Overall, this study provides the detailed structural analysis of RRM domain of RBM3, its interaction with RNA and the molecular basis of its temperature-dependent oligomerization.


  • Organizational Affiliation

    School of Bioscience, Indian Institute of Technology Kharagpur, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 384Homo sapiensMutation(s): 0 
Gene Names: RBM3RNPL
UniProt & NIH Common Fund Data Resources
Find proteins for P98179 (Homo sapiens)
Explore P98179 
Go to UniProtKB:  P98179
PHAROS:  P98179
GTEx:  ENSG00000102317 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98179
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR34319/MED/29/1488/2019
Department of Science & Technology (DST, India)IndiaSR/WOS-A/LS-659/2016

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references