6VYP

Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.99 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate.

Kim, S.A., Zhu, J., Yennawar, N., Eek, P., Tan, S.

(2020) Mol Cell 78: 903

  • DOI: 10.1016/j.molcel.2020.04.019
  • Primary Citation of Related Structures:  
    6VYP

  • PubMed Abstract: 

    • LSD1 (lysine specific demethylase; also known as KDM1A), the first histone demethylase discovered, regulates cell-fate determination and is overexpressed in multiple cancers. LSD1 demethylates histone H3 Lys4, an epigenetic mark for active genes, but ...

    LSD1 (lysine specific demethylase; also known as KDM1A), the first histone demethylase discovered, regulates cell-fate determination and is overexpressed in multiple cancers. LSD1 demethylates histone H3 Lys4, an epigenetic mark for active genes, but requires the CoREST repressor to act on nucleosome substrates. To understand how an accessory subunit (CoREST) enables a chromatin enzyme (LSD1) to function on a nucleosome and not just histones, we have determined the crystal structure of the LSD1/CoREST complex bound to a 191-bp nucleosome. We find that the LSD1 catalytic domain binds extranucleosomal DNA and is unexpectedly positioned 100 Å away from the nucleosome core. CoREST makes critical contacts with both histone and DNA components of the nucleosome, explaining its essential function in demethylating nucleosome substrates. Our studies also show that the LSD1(K661A) frequently used as a catalytically inactive mutant in vivo (based on in vitro peptide studies) actually retains substantial H3K4 demethylase activity on nucleosome substrates.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address: sxt30@psu.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3A, E, a, e135Xenopus laevisMutation(s): 1 
Gene Names: XELAEV_18002543mg
Find proteins for P84233 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F, b, f102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G, c, g129Xenopus laevisMutation(s): 2 
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H, d, h122Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1AK, M, k, m684Homo sapiensMutation(s): 3 
Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1
EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
Find proteins for O60341 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  O60341
GTEx  ENSG00000004487
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
REST corepressor 1L, N, l, n157Homo sapiensMutation(s): 0 
Gene Names: RCOR1, KIAA0071, RCOR
Find proteins for Q9UKL0 (Homo sapiens)
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PHAROS  Q9UKL0
GTEx  ENSG00000089902
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (191-MER)I, i191synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (191-MER)J, j191synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
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K, M, k, m
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.99 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.771α = 90
b = 335.77β = 91.07
c = 174.633γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM088236
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111651
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127034

Revision History 

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references