8VPQ: LSD1-CoREST-HDAC1

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML. Determined by electron microscopy at 3.3 Å resolution. Released 27 Nov 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,090
Mol. weight: 229.73 kDa
Ligands: IHP, ZN
Released: 27 Nov 2024

Explore 8VPQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VPQ contains 54 α-helices and 97 β-strands across 4 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: 16 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
β-strand	30	1	2
β-strand	34-38	5	2
α-helix	42-53	12
β-strand	63-67	5	3
β-strand	70-74	5	3
α-helix	76-82	7
α-helix	85-89	5
β-strand	101-104	4	3
α-helix	112-119	8
β-strand	123-127	5	4
α-helix	131-140	10
α-helix	144-155	12
α-helix	160-162	3
α-helix	164-172	9
α-helix	176-188	13
α-helix	204-211	8
β-strand	216	1	5
α-helix	217-219	3
α-helix	221-229	9
α-helix	240-243	4
β-strand	250	1	5
β-strand	255-261	7	6
β-strand	271-276	6	6
β-strand	280-283	4	6
β-strand	295-299	5	7
β-strand	302-306	5	7
β-strand	317-319	3	7
β-strand	326-328	3	7
α-helix	330-332	3
β-strand	337	1	8
β-strand	340-344	5	9
β-strand	349-353	5	9
β-strand	355-357	3	8
β-strand	359-363	5	8
β-strand	365	1	10
β-strand	367-370	4	9
β-strand	376	1	9
α-helix	380	1
β-strand	381	1	10
α-helix	382	1
β-strand	387	1	11
β-strand	390-394	5	12
β-strand	397-401	5	12
β-strand	404-406	3	11
β-strand	412-414	3	11
β-strand	418-422	5	12
β-strand	427-430	4	12
β-strand	442-446	5	13
β-strand	449-453	5	13
β-strand	460-462	3	13
β-strand	463	1	14
β-strand	468	1	14
β-strand	471	1	13
β-strand	485-489	5	15
β-strand	494-498	5	15
β-strand	508-512	5	15
β-strand	517-520	4	15
β-strand	530-535	6	6

Chain B: 16 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	4
β-strand	34-38	5	4
α-helix	42-53	12
β-strand	63-67	5	16
β-strand	70-74	5	16
α-helix	76-80	5
α-helix	84-90	7
β-strand	101-104	4	16
α-helix	112-116	5
α-helix	117-121	5
β-strand	123-127	5	2
α-helix	132-141	10
α-helix	144-156	13
α-helix	163-169	7
α-helix	176-187	12
α-helix	191-193	3
α-helix	204-211	8
α-helix	217-219	3
α-helix	222-229	8
α-helix	233-236	4
α-helix	237-239	3
β-strand	258-261	4	17
β-strand	268-271	4	17
β-strand	275	1	18
β-strand	281	1	18
β-strand	289	1	17
β-strand	295-299	5	19
β-strand	302-306	5	19
β-strand	316-319	4	19
α-helix	330-332	3
β-strand	337	1	20
β-strand	340-342	3	21
β-strand	350-353	4	21
β-strand	356	1	20
β-strand	362	1	20
β-strand	367-370	4	21
β-strand	375-378	4	21
β-strand	386	1	22
β-strand	390-394	5	23
β-strand	397-401	5	23
β-strand	405-406	2	22
β-strand	412-413	2	22
β-strand	418-421	4	23
β-strand	430	1	23
β-strand	442-446	5	1
β-strand	449-453	5	1
β-strand	460-463	4	1
β-strand	468-470	3	1
β-strand	486-488	3	24
β-strand	494-497	4	24
β-strand	509-511	3	24
β-strand	519	1	24
β-strand	531-534	4	17

Chain C: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	25
α-helix	19-21	3
α-helix	33-42	10
β-strand	52-55	4	25
α-helix	70-77	8
α-helix	89-93	5
β-strand	96	1	26
β-strand	100	1	26
α-helix	107-124	18
β-strand	131-134	4	25
β-strand	143	1	27
β-strand	146	1	27
β-strand	148	1	28
β-strand	151	1	28
α-helix	155-163	9
β-strand	170-174	5	25
α-helix	181-186	6
β-strand	193-200	8	25
β-strand	223-228	6	25
α-helix	234-252	19
β-strand	256-260	5	25
α-helix	278-289	12
β-strand	295-298	4	25
α-helix	305-319	15
β-strand	327	1	29
α-helix	328-329	2
β-strand	342	1	29
α-helix	350-352	3
α-helix	357-370	14

Chain D: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	16-18	3
α-helix	21-24	4
β-strand	31-32	2	25
α-helix	42-54	13
α-helix	62-68	7
α-helix	74-79	6
α-helix	93-105	13
α-helix	110-113	4
α-helix	123-130	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Kelch repeat and BTB domain-containing protein 4	A, B	protein	536	Homo sapiens	Q9NVX7 (AlphaFold model)
Histone deacetylase 1	C	protein	482	Homo sapiens	Q13547 (AlphaFold model)
REST corepressor 1	D	protein	485	Homo sapiens	Q9UKL0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8VPQ_1 Isoform 2 of Kelch repeat and BTB domain-containing protein 4 (chains A, B)
MKGGNADSWQREKLASMESPEEPGASMDENYFVNYTFKDRSHSGRVAQGIMKLCLEEELF
ADVTISVEGREFQLHRLVLSAQSCFFRSMFTSNLKEAHNRVIVLQDVSESVFQLLVDYIY
HGTVKLRAEELQEIYEVSDMYQLTSLFEECSRFLARTVQVGNCLQVMWLADRHSDPELYT
AAKHCAKTHLAQLQNTEEFLHLPHRLLTDIISDGVPCSQNPTEAIEAWINFNKEEREAFA
ESLRTSLKEIGENVHIYLIGKESSRTHSLAVSLHCAEDDSISVSGQNSLCHQITAACKHG
GDLYVVGGSTTYMLRMWKCNNATVDWEWCAPLPRDRLQHTLVSVPGKDAIYSLGGKTLQD
TLSNAVIYYRVGDNVWTETTQLEVAVSGAAGANLNGIIYLLGGEENDLDFFTKPSRLIQC
FDTETDKCHVKPYVLPFAGRMHAAVHKDLVFIVAEGDSLVCYNPLLDSFTRLCLPEAWSS
APSLWKIASCNGSIYVFRDRYKKGDANTYKLDPATSAVTVTRGIKVLLTNLQFVLA

Sequence of entity 2 (C), FASTA

>8VPQ_2 Histone deacetylase 1 (chains C)
MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN
AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS
AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG
DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI
FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG
GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE
KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF
SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK
LA

Sequence of entity 3 (D), FASTA

>8VPQ_3 REST corepressor 1 (chains D)
MPAMVEKGPEVSGKRRGRNNAAASASAAAASAAASAACASPAATAASGAAASSASAAAAS
AAAAPNNGQNKSLAAAAPNGNSSSNSWEEGSSGSSSDEEHGGGGMRVGPQYQAVVPDFDP
AKLARRSQERDNLGMLVWSPNQNLSEAKLDEYIAIAKEKHGYNMEQALGMLFWHKHNIEK
SLADLPNFTPFPDEWTVEDKVLFEQAFSFHGKTFHRIQQMLPDKSIASLVKFYYSWKKTR
TKTSVMDRHARKQKREREESEDELEEANGNNPIDIEVDQNKESKKEVPPTETVPQVKKEK
HSTQAKNRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNS
ALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQV
KNFFVNYRRRFNIDEVLQEWEAEHGKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVR
YASAS

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
ZN	Zinc ion	Zn	1

Primary citation

Converging mechanism of UM171 and KBTBD4 neomorphic cancer mutations. Xie, X., Zhang, O., Yeo, M.J.R. et al. Nature (2025) 639:241-249. DOI 10.1038/s41586-024-08533-3 · PubMed

Other PDB entries of the same protein (UniProt Q9NVX7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GGM 2.71 Å, Cryo-EM structure of KBTBD4 P313PRR mutant-HDAC2 2:2 complex
9DTQ 2.87 Å, The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant
9GGN 2.9 Å, Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171
9GGL 3.13 Å, Cryo-EM structure of KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171
9I2C 3.3 Å, Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue…
8VRT 3.42 Å, The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant
8VOJ 3.77 Å, The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and…
9DTG 3.83 Å, The cryo-EM structure of apo KBTBD4
2EQX Solution structure of the BACK domain of Kelch repeat and BTB domain-containing protein 4

Browse structure collections

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