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
  • Structures With Same Primary Citation

  • 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: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, b, f
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G, c, g
129Xenopus laevisMutation(s): 2 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Protein Feature View
  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1A
K, M, k, m
684Homo sapiensMutation(s): 3 
Gene Names: KDM1AAOF2KDM1KIAA0601LSD1
EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
Find proteins for O60341 (Homo sapiens)
Go to UniProtKB:  O60341
NIH Common Fund Data Resources
PHAROS  O60341
Protein Feature View
  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E, a, e
135Xenopus laevisMutation(s): 1 
Gene Names: XELAEV_18002543mg
Find proteins for A0A310TTQ1 (Xenopus laevis)
Go to UniProtKB:  A0A310TTQ1
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H, d, h
122Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Protein Feature View
  • Reference Sequence

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
REST corepressor 1
L, N, l, n
157Homo sapiensMutation(s): 0 
Gene Names: RCOR1KIAA0071RCOR
Find proteins for Q9UKL0 (Homo sapiens)
Go to UniProtKB:  Q9UKL0
NIH Common Fund Data Resources
PHAROS  Q9UKL0
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganism
DNA (191-MER)I, i191synthetic construct

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA (191-MER)J, j191synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
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

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 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