3UJM

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
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2012.02.140
Primary Citation of 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. tv@farma.ku.dk

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rasputin	A, B	120	Drosophila melanogaster	Mutation(s): 0 Gene Names: rin, CG9412
UniProt
Find proteins for Q9VFT4 (Drosophila melanogaster) Explore Q9VFT4 Go to UniProtKB: Q9VFT4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9VFT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.242
R-Value Work: 0.197
R-Value Observed: 0.199
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Vognsen, T.

Kristensen, O.

Revision History (Full details and data files)

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