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 3PUR | pdb_00003pur

CEKDM7A from C.Elegans, complex with D-2-HG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.251 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3PUR

This is version 1.3 of the entry. See complete history. 

Literature

Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases

Xu, W., Yang, H., Liu, Y., Yang, Y., Wang, P., Kim, S.-H., Ito, S., Yang, C., Wang, P., Xiao, M.-T., Liu, L.-X., Jiang, W.-Q., Liu, J., Zhang, J.-Y., Wang, B., Frye, S., Zhang, Y., Xu, Y.-H., Lei, Q.-Y., Guan, K.-L., Zhao, S.-M., Xiong, Y.

(2011) Cancer Cell 19: 17-30

  • DOI: https://doi.org/10.1016/j.ccr.2010.12.014
  • Primary Citation Related Structures: 
    3PUQ, 3PUR

  • PubMed Abstract: 

    IDH1 and IDH2 mutations occur frequently in gliomas and acute myeloid leukemia, leading to simultaneous loss and gain of activities in the production of α-ketoglutarate (α-KG) and 2-hydroxyglutarate (2-HG), respectively. Here we demonstrate that 2-HG is a competitive inhibitor of multiple α-KG-dependent dioxygenases, including histone demethylases and the TET family of 5-methlycytosine (5mC) hydroxylases. 2-HG occupies the same space as α-KG does in the active site of histone demethylases. Ectopic expression of tumor-derived IDH1 and IDH2 mutants inhibits histone demethylation and 5mC hydroxylation. In glioma, IDH1 mutations are associated with increased histone methylation and decreased 5-hydroxylmethylcytosine (5hmC). Hence, tumor-derived IDH1 and IDH2 mutations reduce α-KG and accumulate an α-KG antagonist, 2-HG, leading to genome-wide histone and DNA methylation alterations.


  • Organizational Affiliation: 
    • State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Medical School, Fudan University, Shanghai 20032, China.

Macromolecule Content 

  • Total Structure Weight: 124.56 kDa 
  • Atom Count: 8,399 
  • Modeled Residue Count: 979 
  • Deposited Residue Count: 1,056 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 7 homologA,
B [auth C]
528Caenorhabditis elegansMutation(s): 0 
Gene Names: F29B9.2
EC: 1.14.11.27 (PDB Primary Data), 1.14.11 (UniProt)
UniProt
Find proteins for Q9GYI0 (Caenorhabditis elegans)
Explore Q9GYI0 
Go to UniProtKB:  Q9GYI0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GYI0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2HG

Query on 2HG



Download:Ideal Coordinates CCD File
F [auth A],
J [auth C]
(2R)-2-hydroxypentanedioic acid
C5 H8 O5
HWXBTNAVRSUOJR-GSVOUGTGSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth C],
I [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
C [auth A],
G [auth C]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.009α = 90
b = 144.086β = 106.22
c = 78.087γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations