6LE1

Structure of RRM2 domain of DND1 protein

• PDB DOI: https://doi.org/10.2210/pdb6LE1/pdb

• 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)

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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 

Literature

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

Kumari, P., Bhavesh, N.S.

(2021) Protein Sci 30: 1184-1195

• PubMed: 33860980 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 10.9 kDa 
• Atom Count: 692 
• Modelled Residue Count: 89 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dead end protein homolog 1	A	100	Homo sapiens	Mutation(s): 0  Gene Names: DND1, RBMS4
UniProt
Find proteins for Q8IYX4 (Homo sapiens) Explore Q8IYX4  Go to UniProtKB:  Q8IYX4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 44.615	α = 90
b = 44.615	β = 90
c = 111.332	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Kumari, P., Bhavesh, N.S.

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

Revision History  

• 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