2XMR | pdb_00002xmr

Crystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.232 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2XMR

This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Human Ndrg2 Protein Provides Insight Into its Role as a Tumor Suppressor.

Hwang, J.Kim, Y.Kang, H.B.Jaroszewski, L.Deacon, A.Lee, H.Choi, W.C.Kim, K.J.Kim, C.H.Kang, B.S.Lee, J.O.Oh, T.K.Kim, J.W.Wilson, I.A.Kim, M.H.

(2011) J Biological Chem 286: 12450

  • DOI: https://doi.org/10.1074/jbc.M110.170803
  • Primary Citation Related Structures: 
    2QMQ, 2XMQ, 2XMR, 2XMS

  • PubMed Abstract: 

    Considerable attention has recently been paid to the N-Myc downstream-regulated gene (NDRG) family because of its potential as a tumor suppressor in many human cancers. Primary amino acid sequence information suggests that the NDRG family proteins may belong to the α/β-hydrolase (ABH) superfamily; however, their functional role has not yet been determined. Here, we present the crystal structures of the human and mouse NDRG2 proteins determined at 2.0 and 1.7 Å resolution, respectively. Both NDRG2 proteins show remarkable structural similarity to the ABH superfamily, despite limited sequence similarity. Structural analysis suggests that NDRG2 is a nonenzymatic member of the ABH superfamily, because it lacks the catalytic signature residues and has an occluded substrate-binding site. Several conserved structural features suggest NDRG may be involved in molecular interactions. Mutagenesis data based on the structural analysis support a crucial role for helix α6 in the suppression of TCF/β-catenin signaling in the tumorigenesis of human colorectal cancer, via a molecular interaction.


  • Organizational Affiliation
    • Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.

Macromolecule Content 

  • Total Structure Weight: 94.16 kDa 
  • Atom Count: 7,032 
  • Modeled Residue Count: 843 
  • Deposited Residue Count: 843 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN NDRG2
A, B, C
281Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UN36 (Homo sapiens)
Explore Q9UN36 
Go to UniProtKB:  Q9UN36
PHAROS:  Q9UN36
GTEx:  ENSG00000165795 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UN36
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.232 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.232α = 90
b = 88.049β = 90
c = 126.907γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Database references, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description