Human JMJD5 in complex with MN and 2OG.

Experimental Data Snapshot

  • Resolution: 2.54 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


JMJD5 is a human arginyl C-3 hydroxylase.

Wilkins, S.E.Islam, S.Gannon, J.M.Markolovic, S.Hopkinson, R.J.Ge, W.Schofield, C.J.Chowdhury, R.

(2018) Nat Commun 9: 1180-1180

  • DOI: https://doi.org/10.1038/s41467-018-03410-w
  • Primary Citation of Related Structures:  
    6F4M, 6F4N, 6F4O, 6F4P, 6F4Q, 6F4R, 6F4S, 6F4T

  • PubMed Abstract: 

    Oxygenase-catalysed post-translational modifications of basic protein residues, including lysyl hydroxylations and N ε -methyl lysyl demethylations, have important cellular roles. Jumonji-C (JmjC) domain-containing protein 5 (JMJD5), which genetic studies reveal is essential in animal development, is reported as a histone N ε -methyl lysine demethylase (KDM). Here we report how extensive screening with peptides based on JMJD5 interacting proteins led to the finding that JMJD5 catalyses stereoselective C-3 hydroxylation of arginine residues in sequences from human regulator of chromosome condensation domain-containing protein 1 (RCCD1) and ribosomal protein S6 (RPS6). High-resolution crystallographic analyses reveal overall fold, active site and substrate binding/product release features supporting the assignment of JMJD5 as an arginine hydroxylase rather than a KDM. The results will be useful in the development of selective oxygenase inhibitors for the treatment of cancer and genetic diseases.

  • Organizational Affiliation

    The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
JmjC domain-containing protein 5
A, B
271Homo sapiensMutation(s): 0 
Gene Names: KDM8JMJD5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N371 (Homo sapiens)
Explore Q8N371 
Go to UniProtKB:  Q8N371
GTEx:  ENSG00000155666 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N371
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.54 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.002α = 90
b = 68.002β = 90
c = 267.898γ = 120
Software Package:
Software NamePurpose
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: 2018-04-04
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description