8VRT: LSD1-CoREST-HDAC1

The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant. Determined by electron microscopy at 3.42 Å resolution. Released 27 Nov 2024.

Method: Electron microscopy
Resolution: 3.42 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,240
Mol. weight: 218.8 kDa
Ligands: ZN, IHP
Released: 27 Nov 2024

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

Secondary structure: helices and β-sheets

8VRT contains 70 α-helices and 98 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: 20 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	30	1	2
β-strand	34-38	5	2
α-helix	42-51	10
α-helix	52-57	6
β-strand	63-67	5	3
β-strand	70-74	5	3
α-helix	76-82	7
α-helix	84-90	7
α-helix	95-98	4
β-strand	101-104	4	3
α-helix	109-120	12
β-strand	123-127	5	4
α-helix	131-140	10
α-helix	144-156	13
α-helix	163-172	10
α-helix	176-187	12
α-helix	191-193	3
α-helix	197-200	4
α-helix	204-212	9
β-strand	215-216	2	5
α-helix	217-219	3
α-helix	221-231	11
α-helix	233-236	4
α-helix	240-245	6
β-strand	249-250	2	5
β-strand	255-261	7	6
β-strand	268-275	8	6
β-strand	281-289	9	6
β-strand	293-299	7	7
β-strand	302-307	6	7
β-strand	315-320	6	7
β-strand	325-328	4	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	356	1	8
β-strand	362	1	8
β-strand	366-370	5	9
β-strand	375-379	5	9
α-helix	380-382	3
β-strand	387	1	10
β-strand	390-394	5	11
β-strand	397-401	5	11
β-strand	403	1	12
β-strand	404-407	4	10
β-strand	411-414	4	10
β-strand	417-422	6	11
β-strand	427-434	8	11
β-strand	439	1	12
β-strand	441-446	6	13
β-strand	449-454	6	13
β-strand	458-463	6	13
β-strand	468-472	5	13
α-helix	476-480	5
β-strand	485-490	6	14
β-strand	493-498	6	14
β-strand	500	1	6
β-strand	502	1	15
β-strand	505	1	15
β-strand	508-512	5	14
β-strand	517-520	4	14
β-strand	530-534	5	6

Chain B: 22 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	4
β-strand	34-38	5	4
α-helix	42-51	10
α-helix	52-56	5
β-strand	63-67	5	16
β-strand	70-74	5	16
α-helix	76-82	7
α-helix	84-90	7
α-helix	95-98	4
β-strand	101-104	4	16
α-helix	109-121	13
β-strand	123-127	5	2
α-helix	128-130	3
α-helix	131-140	10
α-helix	144-157	14
α-helix	163-173	11
α-helix	176-187	12
α-helix	192-195	4
α-helix	197-201	5
α-helix	204-212	9
β-strand	215-216	2	17
α-helix	217-219	3
α-helix	221-231	11
α-helix	237-239	3
α-helix	240-246	7
β-strand	249-250	2	17
β-strand	255-261	7	18
β-strand	268-275	8	18
β-strand	281-289	9	18
β-strand	295-299	5	19
β-strand	302-306	5	19
β-strand	316-319	4	19
β-strand	327-329	3	19
α-helix	330-332	3
β-strand	337	1	20
β-strand	340-344	5	21
β-strand	349-353	5	21
β-strand	356	1	20
β-strand	366-370	5	21
β-strand	375-378	4	21
α-helix	380-382	3
β-strand	390-394	5	22
β-strand	397-401	5	22
β-strand	404-406	3	23
β-strand	412-414	3	23
β-strand	417-422	6	22
β-strand	427-434	8	22
β-strand	441-446	6	1
β-strand	449-454	6	1
β-strand	458-463	6	1
β-strand	468-472	5	1
α-helix	473	1
α-helix	476-480	5
β-strand	485-490	6	24
β-strand	493-498	6	24
β-strand	500	1	18
β-strand	502	1	25
β-strand	505	1	25
β-strand	508-512	5	24
β-strand	517-520	4	24
β-strand	530-535	6	18

Chain C: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	26
α-helix	19-21	3
α-helix	34-45	12
α-helix	47-50	4
β-strand	52-56	5	26
α-helix	61-64	4
α-helix	70-78	9
α-helix	81-87	7
α-helix	88-94	7
α-helix	106-125	20
β-strand	131-134	4	26
β-strand	148	1	27
β-strand	151	1	27
α-helix	155-163	9
β-strand	170-174	5	26
α-helix	181-186	6
β-strand	193-200	8	26
α-helix	217-219	3
β-strand	223-228	6	26
α-helix	234-252	19
β-strand	256-260	5	26
β-strand	266	1	28
β-strand	276	1	28
α-helix	278-289	12
β-strand	295-298	4	26
α-helix	305-319	15
β-strand	327	1	29
α-helix	328-330	3
α-helix	334-337	4
β-strand	342	1	29
α-helix	356-371	16
α-helix	374-375	2

Chain D: 10 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	16-18	3
α-helix	19-25	7
α-helix	27-28	2
β-strand	30-34	5	26
α-helix	42-55	14
α-helix	60-69	10
α-helix	74-80	7
α-helix	93-106	14
α-helix	110-116	7
α-helix	122-132	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kelch repeat and BTB domain-containing protein 4	A, B	protein	520	Homo sapiens	Q9NVX7 (AlphaFold model)
Histone deacetylase 1	C	protein	482	Homo sapiens	Q13547 (AlphaFold model)
REST corepressor 1	D	protein	401	Homo sapiens	Q9UKL0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8VRT_1 Kelch repeat and BTB domain-containing protein 4 (chains A, B)
MESPEEPGASMDENYFVNYTFKDRSHSGRVAQGIMKLCLEEELFADVTISVEGREFQLHR
LVLSAQSCFFRSMFTSNLKEAHNRVIVLQDVSESVFQLLVDYIYHGTVKLRAEELQEIYE
VSDMYQLTSLFEECSRFLARTVQVGNCLQVMWLADRHSDPELYTAAKHCAKTHLAQLQNT
EEFLHLPHRLLTDIISDGVPCSQNPTEAIEAWINFNKEEREAFAESLRTSLKEIGENVHI
YLIGKESSRTHSLAVSLHCAEDDSISVSGQNSLCHQITAACKHGGDLYVVGGSIPRPRRM
WKCNNATVDWEWCAPLPRDRLQHTLVSVPGKDAIYSLGGKTLQDTLSNAVIYYRVGDNVW
TETTQLEVAVSGAAGANLNGIIYLLGGEENDLDFFTKPSRLIQCFDTETDKCHVKPYVLP
FAGRMHAAVHKDLVFIVAEGDSLVCYNPLLDSFTRLCLPEAWSSAPSLWKIASCNGSIYV
FRDRYKKGDANTYKLDPATSAVTVTRGIKVLLTNLQFVLA

Sequence of entity 2 (C), FASTA

>8VRT_2 Histone deacetylase 1 (chains C)
MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN
AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS
AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG
DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI
FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG
GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE
KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF
SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK
LA

Sequence of entity 3 (D), FASTA

>8VRT_3 REST corepressor 1 (chains D)
MSWEEGSSGSSSDEEHGGGGMRVGPQYQAVVPDFDPAKLARRSQERDNLGMLVWSPNQNL
SEAKLDEYIAIAKEKHGYNMEQALGMLFWHKHNIEKSLADLPNFTPFPDEWTVEDKVLFE
QAFSFHGKTFHRIQQMLPDKSIASLVKFYYSWKKTRTKTSVMDRHARKQKREREESEDEL
EEANGNNPIDIEVDQNKESKKEVPPTETVPQVKKEKHSTQAKNRAKRKPPKGMFLSQEDV
EAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNA
RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAEH
GKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVRYASAS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	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
8VPQ 3.3 Å, The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML
9I2C 3.3 Å, Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue…
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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