2V1D: Lysine-specific histone demethylase 1

Structural basis of LSD1-CoREST selectivity in histone H3 recognition. Determined by X-ray diffraction at 3.1 Å resolution. Released 29 May 2007.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 6,460
Mol. weight: 104.57 kDa
Ligands: FAD
Released: 29 May 2007

Explore 2V1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2V1D contains 39 α-helices and 36 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 31 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	174-180	7
α-helix	190-195	6
α-helix	197-201	5
α-helix	204-223	20
β-strand	227	1	1
α-helix	231-237	7
α-helix	242-244	3
α-helix	246-258	13
β-strand	268	1	1
β-strand	280-284	5	2
α-helix	288-299	12
β-strand	303-307	5	2
β-strand	319-322	4	3
β-strand	325-328	4	3
β-strand	333-334	2	4
β-strand	338	1	5
α-helix	341-348	8
β-strand	353-355	3	4
α-helix	356-357	2
β-strand	363	1	6
β-strand	369	1	6
α-helix	370-371	2
α-helix	372-394	23
β-strand	400-401	2	7
β-strand	404-405	2	7
α-helix	406	1
β-strand	407	1	8
α-helix	408-467	60
α-helix	469	1
α-helix	474-511	38
α-helix	523-539	17
β-strand	547	1	9
β-strand	548	1	8
α-helix	556-558	3
β-strand	561	1	5
β-strand	565-567	3	4
α-helix	573-579	7
β-strand	584-585	2	2
β-strand	588-596	9	10
β-strand	599-606	8	10
β-strand	613-618	6	10
β-strand	620-623	4	2
α-helix	627-631	5
β-strand	638-640	3	10
α-helix	642-644	3
α-helix	645-653	9
β-strand	655-656	2	11
β-strand	660-665	6	12
β-strand	677-679	3	12
β-strand	693-696	4	12
β-strand	702-707	6	12
α-helix	709-715	7
α-helix	720-735	16
α-helix	741-743	3
β-strand	745-748	4	12
β-strand	762-763	2	11
β-strand	765	1	9
β-strand	766	1	13
β-strand	768	1	13
α-helix	770-777	8
β-strand	780	1	2
α-helix	782-784	3
α-helix	790-794	5
β-strand	796-798	3	2
α-helix	801-803	3
α-helix	811-829	19
α-helix	833-835	3

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	318-325	8
α-helix	330-362	33
α-helix	368-370	3
α-helix	385-398	14
α-helix	402-409	8
α-helix	414-423	10
α-helix	430-438	9

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1	A	protein	730	HOMO SAPIENS	O60341 (AlphaFold model)
Rest corepressor 1	B	protein	178	HOMO SAPIENS	Q9UKL0 (AlphaFold model)
Histone H3.1T	C	protein	21	HOMO SAPIENS	Q16695 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2V1D_1 LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 (chains A)
MDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQSR
LPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPY
NSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGM
DVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPL
YEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKH
VKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKS
KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANAT
PLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEV
IAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKV
VLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDV
IVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITP
GPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATP
GVPAQQSPSM

Sequence of entity 2 (B), FASTA

>2V1D_2 REST COREPRESSOR 1 (chains B)
RAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLD
GGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNY
RRRFNIDEVLQEWEAEHGKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVRYASAS

Sequence of entity 3 (C), FASTA

>2V1D_3 HISTONE H3.1T (chains C)
ARTMQTARKSTGGKAPRKQLA

Ligands and cofactors

ID	Name	Formula	Copies
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	1

Primary citation

Structural Basis of Lsd1-Corest Selectivity in Histone H3 Recognition. Forneris, F., Binda, C., Adamo, A. et al. J Biol Chem (2007) 282:20070. DOI 10.1074/JBC.C700100200 · PubMed

Other PDB entries of the same protein (UniProt O60341 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E1F 1.16 Å, Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1
5IT3 1.4 Å, Swirm domain of human Lsd1
5AFW 1.6 Å, Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation
7JK7 1.96 Å, Crystal structure of Importin alpha 2 in complex with LSD1 NLS S111E mutant
7JJM 2.06 Å, Crystal structure of Importin alpha 2 in complex with LSD1 NLS
2Z3Y 2.25 Å, Crystal structure of Lysine-specific demethylase1
2Z5U 2.25 Å, Crystal structure of Lysine-specific histone demethylase 1
6KGO 2.25 Å, LSD1-S2157 five-membered ring adduct model
6KGP 2.25 Å, LSD1-S2157 N5 adduct model
7E0G 2.25 Å, Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct
7XW8 2.28 Å, Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer,…
2DW4 2.3 Å, Crystal structure of human LSD1 at 2.3 A resolution

Browse structure collections

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