Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.41 kDa 
• Atom Count: 507 
• Residue Count: 65 
• Unique protein chains: 2

2MNZ

NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa)

• DOI: 10.2210/pdb2MNZ/pdb
• BMRB: 19914

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-16 Released: 2014-08-06 
• Deposition Author(s): Zhang, Y., Yang, H.R., Guo, X., Rong, N.Y., Song, Y.J., Xu, Y.W., Lan, W.X., Xu, Y.H., Cao, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B

Zhang, Y., Yang, H.R., Guo, X., Rong, N.Y., Song, Y.J., Xu, Y.W., Lan, W.X., Zhang, X., Liu, M., Xu, Y.H., Cao, C.

(2014) Protein Cell 

• PubMed: 24952722 
• DOI: 10.1007/s13238-014-0078-4
• Primary Citation of Related Structures:  
  2MNZ, 2MNY


• PubMed Abstract: 
  

KDM5B is a histone H3K4me2/3 demethylase. The PHD1 domain of KDM5B is critical for demethylation, but the mechanism underlying the action of this domain is unclear. In this paper, we observed that PHD1KDM5B interacts with unmethylated H3K4me0. Our NMR structure of PHD1KDM5B in complex with H3K4me0 revealed that the binding mode is slightly different from that of other reported PHD fingers. The disruption of this interaction by double mutations on the residues in the interface (L325A/D328A) decreases the H3K4me2/3 demethylation activity of KDM5B in cells by approximately 50% and increases the transcriptional repression of tumor suppressor genes by approximately twofold. These findings imply that PHD1KDM5B may help maintain KDM5B at target genes to mediate the demethylation activities of KDM5B.

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Organizational Affiliation: 

State Key Laboratory of Bio-organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5B	A	55	Homo sapiens	Mutation(s): 0  Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for Q9UGL1 (Homo sapiens) Explore Q9UGL1  Go to UniProtKB:  Q9UGL1
NIH Common Fund Data Resources
PHAROS:  Q9UGL1 GTEx:  ENSG00000117139

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K4me0	B	10	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2MNZ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-16 
• Released Date: 2014-08-06 
Deposition Author(s): Zhang, Y., Yang, H.R., Guo, X., Rong, N.Y., Song, Y.J., Xu, Y.W., Lan, W.X., Xu, Y.H., Cao, C.

Revision History 

• Version 1.0: 2014-08-06
  Type: Initial release