7UV9

KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of paralog-specific KDM2A/B nucleosome recognition.

Spangler, C.J.Skrajna, A.Foley, C.A.Nguyen, A.Budziszewski, G.R.Azzam, D.N.Arteaga, E.C.Simmons, H.C.Smith, C.B.Wesley, N.A.Wilkerson, E.M.McPherson, J.E.Kireev, D.James, L.I.Frye, S.V.Goldfarb, D.McGinty, R.K.

(2023) Nat Chem Biol 19: 624-632

  • DOI: https://doi.org/10.1038/s41589-023-01256-y
  • Primary Citation of Related Structures:  
    7UV9, 7UVA

  • PubMed Abstract: 

    The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. To define the molecular basis of acidic patch recognition proteome wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. Despite fundamental roles in transcriptional repression in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any related JumonjiC (JmjC) domain lysine demethylase, remain unclear. We used a covalent conjugate between H3K36 and a demethylase inhibitor to solve cryogenic electron microscopy structures of KDM2A and KDM2B trapped in action on a nucleosome substrate. Our structures show that KDM2-nucleosome binding is paralog specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation.


  • Organizational Affiliation

    Department of Chemistry, University of Missouri, Columbia, MO, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Homo sapiensMutation(s): 1 
Gene Names: H3C15HIST2H3AH3C14H3F2H3FMHIST2H3CH3C13HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens)
Explore Q71DI3 
Go to UniProtKB:  Q71DI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ71DI3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
129Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S8 (Homo sapiens)
Explore P0C0S8 
Go to UniProtKB:  P0C0S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0S8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/I
D, H
125Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62807
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 2A692Homo sapiensMutation(s): 0 
Gene Names: KDM2ACXXC8FBL11FBL7FBXL11JHDM1AKIAA1004
EC: 1.14.11.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2K7 (Homo sapiens)
Explore Q9Y2K7 
Go to UniProtKB:  Q9Y2K7
GTEx:  ENSG00000173120 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2K7
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (185-MER)185synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (185-MER)185synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133498
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesF99CA253730
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM139514
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA010305

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-05-17
    Changes: Database references