6R1U

Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.

Marabelli, C.Marrocco, B.Pilotto, S.Chittori, S.Picaud, S.Marchese, S.Ciossani, G.Forneris, F.Filippakopoulos, P.Schoehn, G.Rhodes, D.Subramaniam, S.Mattevi, A.

(2019) Cell Rep 27: 387-399.e7

  • DOI: 10.1016/j.celrep.2019.03.061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide fromĀ  ...

    LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide fromĀ the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.


    Organizational Affiliation

    The University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada. Electronic address: sriram.subramaniam@ubc.ca.,Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.,Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.,Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK.,Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore.,Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, via Ferrata 9, 27100 Pavia, Italy. Electronic address: andrea.mattevi@unipv.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1B
K
776Homo sapiensMutation(s): 0 
Gene Names: KDM1B (AOF1, C6orf193, LSD2)
EC: 1.-.-.-
Find proteins for Q8NB78 (Homo sapiens)
Go to Gene View: KDM1B
Go to UniProtKB:  Q8NB78
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Putative oxidoreductase GLYR1
L
124Homo sapiensMutation(s): 0 
Gene Names: GLYR1 (HIBDL, NDF, NP60)
EC: 1.-.-.-
Find proteins for Q49A26 (Homo sapiens)
Go to Gene View: GLYR1
Go to UniProtKB:  Q49A26
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Histone H3
M
135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (147-MER)I147synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-MER)J147synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
K
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG-11342

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Data collection, Source and taxonomy, Structure summary