5JIU

The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development.

Hong, S.K.Kim, K.H.Song, E.J.Kim, E.E.

(2016) J Mol Biol 428: 4330-4344

  • DOI: https://doi.org/10.1016/j.jmb.2016.09.004
  • Primary Citation of Related Structures:  
    5JI7, 5JI9, 5JIA, 5JIU

  • PubMed Abstract: 

    RanBPM and RanBP10 are non-canonical members of the Ran binding protein family that lack the Ran binding domain and do not associate with Ran GTPase in vivo. Rather, they have been shown to be scaffolding proteins that are important for a variety of cellular processes, and both of these proteins contain a SPRY domain, which has been implicated in mediating protein-protein interactions with a variety of targets including the DEAD-box containing ATP-dependent RNA helicase (DDX-4). In this study, we have determined the crystal structures of the SPIa and the ryanodine receptor domain and of approximately 70 upstream residues (immediate upstream to SPRY motif) of both RanBPM and RanBP10. They are almost identical, composed of a β-sandwich fold with a set of two helices on each side located at the edge of the sheets. A unique shallow binding surface is formed by highly conserved loops on the surface of the β-sheet with two aspartates on one end, a positive patch on the opposite end, and a tryptophan lining at the bottom of the surface. The 20-mer peptide (residues 228-247) of human DDX-4, an ATP-dependent RNA helicase known to regulate germ cell development, binds to this surface with a K D of ~13μM. The crystal structure of the peptide complex and the mutagenesis studies elucidate how RanBPM can recognize its interaction partners to function in gametogenesis.


  • Organizational Affiliation

    Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu Hwarang-ro 14-gil 5, Seoul 02792, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ran-binding protein 9
A, B
243Homo sapiensMutation(s): 0 
Gene Names: RANBP9RANBPM
UniProt & NIH Common Fund Data Resources
Find proteins for Q96S59 (Homo sapiens)
Explore Q96S59 
Go to UniProtKB:  Q96S59
PHAROS:  Q96S59
GTEx:  ENSG00000010017 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96S59
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX4
C, D
20Mus musculusMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for Q61496 (Mus musculus)
Explore Q61496 
Go to UniProtKB:  Q61496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61496
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.318α = 90
b = 123.318β = 90
c = 91.986γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of ScienceKorea, Republic OfNRF 20110021713
Korea Institute of Science and TechnologyKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description