NDB ID: 6VYP PDB ID: 6VYP 
NAKB(beta): 6VYP
Title:
CRYSTAL STRUCTURE OF THE LSD1/COREST HISTONE DEMETHYLASE BOUND TO ITS NUCLEOSOME SUBSTRATE
Molecular Description:
Histone H3
Histone H4
Histone H2A type 1
Histone H2B 1.1
Lysine-specific histone demethylase 1A
REST corepressor 1/DNA Complex
Deposited:
2020-02-27
Released:
2020-05-27
Structural Keywords:
B DOUBLE HELIX
Nucleic Acid Sequence:
Click to show/hide 2 nucleic acid sequences
Chain I,i
(DA)(DT)(DC)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC)(DC)(
DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(D
C)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC
)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)
(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(
DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(D
T)(DA)(DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT
)(DA)(DT)(DA)(DT) (DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DT)
(DG)(DA) (DA)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DG)(DA)(DT)
Chain J,j
(DA)(DT)(DC)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT) (DG)(DC)(
DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA)(DC)(DA)(DC)(D
G)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DA)(DA)(DT
)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)
(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(
DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(D
G)(DA)(DC)(DC)(DA)(DA)(DT) (DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC
)(DC)(DG)(DG)(DG) (DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)
(DG)(DT) (DA)(DT)(DA)(DG)(DG)(DG)(DT)(DC)(DG)(DA)(DT)
Protein Sequence:
Click to show/hide 6 protein sequences
Chain A,E,a,e
ARTMQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT DLRFQSSAV
MALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Chain C,G,c,g
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAVRN
DEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK
Chain B,F,b,f
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYA
LKRQGRTLYGFGG
Chain D,H,d,h
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHY NKRSTITSR
EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Chain M,m,K,k
GSPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVL VHRVHSYLE
RHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVAD LGAMVVTGLGGNPMAVVS
KQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSL GQALEVVIQLQEKHVKDEQIEHWKKIV
KTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLT ALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSR
DRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVR NGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTASTSQT
FIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKT SAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPI
LLALVAGEAAGIMEAISDAVIVGRCL AILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQ
PIPRLFFAGEHTIRNYP ATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQQSPSM
Chain N,n,L,l
GSPTETVPQVKKEKHSTQAKNRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKL DGGIEPYRL
PEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE
Primary Citation:
Kim, S.A., Zhu, J., Yennawar, N., Eek, P., Tan, S.
Crystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate.
Mol.Cell, 78, pp. 903 - , 2020.
Experimental Information:
X-RAY DIFFRACTION
Space Group:
P 1 21 1
Cell Constants:
a = 103.771 b = 335.77 c = 174.633 (Ångstroms)
α = 90.0 β = 91.07 γ = 90.0 (degrees)
Refinement:
The structure was refined using the PHENIX program.
The R value is 0.2309 for 50660 reflections in
the resolution range 20.17 to 4.99 Ångstroms
with Fobs > 1.34 sigma(Fobs) and with I > 0.0 sigma(I)
