6LE1

Structure of RRM2 domain of DND1 protein

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-11-23 Released: 2020-12-02 
  • Deposition Author(s): Kumari, P., Bhavesh, N.S.
  • Funding Organization(s): International Centre for Genetic Engineering and Biotechnology, New Delhi and Department of Biotechnology (India)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Human DND1-RRM2 forms a non-canonical domain swapped dimer.

Kumari, P.Bhavesh, N.S.

(2021) Protein Sci 30: 1184-1195

  • DOI: 10.1002/pro.4083
  • Primary Citation of Related Structures:  
    6LE1

  • PubMed Abstract: 
  • RNA Recognition Motif (RRM) being the most abundant RNA binding domain in eukaryotes, is a major player in cellular regulation. Several variations in the canonical βαββαβ topology have been observed. We have determined the 2.3 å crystal structure of the human DND1 RRM2 domain ...

    RNA Recognition Motif (RRM) being the most abundant RNA binding domain in eukaryotes, is a major player in cellular regulation. Several variations in the canonical βαββαβ topology have been observed. We have determined the 2.3 å crystal structure of the human DND1 RRM2 domain. The structure revealed an interesting non-canonical RRM fold, which is maintained by the formation of a 3D domain swapped dimer between β 1 and β 4 strands across protomers. We have delineated the structural basis of the stable domain swapped dimer formation using the residue level dynamics of protein explored by NMR spectroscopy and MD simulations. Our structural and dynamics studies substantiate major determinants and molecular basis for domain swapped dimerization observed in the RRM domain.


    Organizational Affiliation

    Transcription Regulation group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dead end protein homolog 1A100Homo sapiensMutation(s): 0 
Gene Names: DND1RBMS4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYX4 (Homo sapiens)
Explore Q8IYX4 
Go to UniProtKB:  Q8IYX4
PHAROS:  Q8IYX4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.615α = 90
b = 44.615β = 90
c = 111.332γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
International Centre for Genetic Engineering and Biotechnology, New Delhi and Department of Biotechnology (India)India--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2021-06-02
    Changes: Database references