7ZRY: PDB entry 7ZRY

Structure of the 2a splicing variant of the full-length human LSD1 bound to CoREST (delta305). Determined by X-ray diffraction at 2.7 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,339
Mol. weight: 115.85 kDa
Ligands: FAD
Released: 3 Aug 2022

Explore 7ZRY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZRY contains 39 α-helices and 36 β-strands across 2 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: 30 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	194-200	7
α-helix	210-215	6
α-helix	217-220	4
α-helix	224-243	20
β-strand	247	1	1
α-helix	251-257	7
α-helix	266-278	13
β-strand	288	1	1
α-helix	292-294	3
β-strand	300-304	5	2
β-strand	307	1	3
α-helix	308-319	12
β-strand	323-327	5	2
β-strand	334	1	3
β-strand	340-342	3	4
β-strand	345-347	3	4
β-strand	353-354	2	5
β-strand	358	1	6
α-helix	361-368	8
β-strand	373-375	3	5
β-strand	383	1	7
β-strand	389	1	7
α-helix	390-391	2
α-helix	392-416	25
β-strand	420	1	8
β-strand	425	1	8
α-helix	426	1
β-strand	427	1	9
α-helix	428-486	59
α-helix	489	1
α-helix	494-531	38
α-helix	543-560	18
β-strand	567	1	10
β-strand	568	1	9
α-helix	576-578	3
α-helix	579-580	2
β-strand	581	1	6
β-strand	585-587	3	5
α-helix	593-599	7
β-strand	603-605	3	2
β-strand	608-616	9	11
β-strand	619-626	8	11
β-strand	633-638	6	11
β-strand	640-643	4	2
α-helix	647-651	5
β-strand	658-660	3	11
α-helix	662-664	3
α-helix	665-673	9
β-strand	675-676	2	12
β-strand	680-685	6	13
β-strand	697-699	3	13
β-strand	713-715	3	13
β-strand	722-727	6	13
α-helix	729-735	7
α-helix	740-755	16
β-strand	765-768	4	13
β-strand	782-783	2	12
β-strand	785	1	10
α-helix	790-797	8
α-helix	799	1
β-strand	800	1	2
α-helix	802-804	3
α-helix	809-814	6
β-strand	816-818	3	2
α-helix	821-823	3
α-helix	831-849	19

Chain B: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	310-311	2
α-helix	318-324	7
α-helix	330-362	33
α-helix	368-370	3
α-helix	371-374	4
α-helix	385-398	14
α-helix	402-409	8
α-helix	414-424	11
α-helix	430-437	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform of Lysine-specific histone demethylase 1A	A	protein	872	Homo sapiens	O60341 (AlphaFold model)
REST corepressor 1	B	protein	178	Homo sapiens	Q9UKL0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7ZRY_1 Isoform of Lysine-specific histone demethylase 1A (chains A)
MLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTP
RKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEY
REMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGQAGGLQD
DSSGGYGDGQASGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGK
VIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGN
PMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNV
LNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQ
QYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVY
LSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAE
GLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFV
PPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKA
PILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGS
YSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLR
EAGRIADQFLGAMYTLPRQATPGVPAQQSPSM

Sequence of entity 2 (B), FASTA

>7ZRY_2 REST corepressor 1 (chains B)
RAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLD
GGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNY
RRRFNIDEVLQEWEAEHGKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVRYASAS

Ligands and cofactors

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

Primary citation

Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism. Astro, V., Ramirez-Calderon, G., Pennucci, R. et al. iScience (2022) 25:104665-104665. DOI 10.1016/j.isci.2022.104665 · 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

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