3UJM | pdb_00003ujm

Crystal structure of the NTF2-like domain of the Drosophila melanogaster Rasputin protein

• PDB DOI: https://doi.org/10.2210/pdb3UJM/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-08 Released: 2012-04-25 
• Deposition Author(s): Vognsen, T., Kristensen, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster.

Vognsen, T., Kristensen, O.

(2012) Biochem Biophys Res Commun 420: 188-192

• PubMed: 22414690 
• DOI: https://doi.org/10.1016/j.bbrc.2012.02.140
• Primary Citation Related Structures: 
  3UJM


• PubMed Abstract: 
  

  The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a β-sheet and three α-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.

---

Organizational Affiliation: 
• Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark. [e-mail]

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)

Macromolecule Content 

• Total Structure Weight: 28.24 kDa 
• Atom Count: 1,991 
• Modeled Residue Count: 234 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rasputin	A, B	120	Drosophila melanogaster	Mutation(s): 0  Gene Names: rin, CG9412 EC: 3.6.4.13
UniProt
Find proteins for Q9VFT4 (Drosophila melanogaster) Explore Q9VFT4  Go to UniProtKB:  Q9VFT4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A], D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.2	α = 90
b = 80.38	β = 92.6
c = 39.2	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
XDS	data scaling
PHASER	phasing
PHENIX	refinement
xia2	data reduction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Vognsen, T., Kristensen, O.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description