5JIU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.054 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1016/j.jmb.2016.09.004
  • Primary Citation of Related Structures:  

  • 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 ...

    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. Electronic address: eunice@kist.re.kr.,Molecular Recognition Research Center, Korea Institute of Science and Technology, Seongbuk-gu Hwarang-ro 14-gil 5, Seoul 02792, Republic of Korea.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ran-binding protein 9
A, B
243Homo sapiensMutation(s): 0 
Gene Names: RANBP9 (RANBPM)
Find proteins for Q96S59 (Homo sapiens)
Go to Gene View: RANBP9
Go to UniProtKB:  Q96S59
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent RNA helicase DDX4
C, D
20Mus musculusMutation(s): 0 
Gene Names: Ddx4 (Mvh, Vasa)
EC: 3.6.4.13
Find proteins for Q61496 (Mus musculus)
Go to UniProtKB:  Q61496
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.054 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 123.318α = 90.00
b = 123.318β = 90.00
c = 91.986γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2016-11-09
    Type: Initial release