9DTQ: HDAC2-CoREST

The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant. Determined by electron microscopy at 2.87 Å resolution. Released 27 Nov 2024.

Method: Electron microscopy
Resolution: 2.87 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,162
Mol. weight: 218.87 kDa
Ligands: IHP
Released: 27 Nov 2024

Explore 9DTQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DTQ contains 68 α-helices and 96 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: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	1
α-helix	20-22	3
α-helix	35-46	12
α-helix	49-51	3
β-strand	53-56	4	1
α-helix	62-65	4
α-helix	71-79	9
α-helix	82-84	3
α-helix	89-95	7
α-helix	107-126	20
β-strand	132-135	4	1
β-strand	149	1	2
β-strand	152	1	2
α-helix	156-164	9
β-strand	171-175	5	1
α-helix	182-187	6
β-strand	194-201	8	1
α-helix	218-220	3
β-strand	224-229	6	1
α-helix	235-253	19
β-strand	257-261	5	1
α-helix	264-266	3
β-strand	267	1	3
β-strand	277	1	3
α-helix	279-289	11
α-helix	290-292	3
β-strand	296-299	4	1
α-helix	306-320	15
β-strand	328	1	4
α-helix	335-338	4
β-strand	343	1	4
α-helix	357-371	15

Chain B: 22 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	5
β-strand	34-38	5	5
α-helix	42-52	11
α-helix	53-57	5
β-strand	63-67	5	6
β-strand	70-74	5	6
α-helix	76-82	7
α-helix	84-91	8
β-strand	102-104	3	6
α-helix	109-121	13
β-strand	123-127	5	7
α-helix	128-130	3
α-helix	131-141	11
α-helix	144-156	13
α-helix	163-172	10
α-helix	176-188	13
α-helix	190-193	4
α-helix	197-200	4
α-helix	204-212	9
β-strand	215-216	2	8
α-helix	217-219	3
α-helix	221-231	11
α-helix	237-239	3
α-helix	240-245	6
β-strand	249-250	2	8
β-strand	256-257	2	9
β-strand	260-262	3	10
β-strand	269	1	10
β-strand	270-275	6	9
β-strand	281-287	7	9
β-strand	292-297	6	11
β-strand	303-308	6	11
β-strand	315-319	5	11
β-strand	327-328	2	11
α-helix	330-332	3
β-strand	337	1	12
β-strand	340-344	5	12
β-strand	349-356	8	12
β-strand	362-370	9	12
β-strand	375-378	4	12
α-helix	380-382	3
β-strand	387	1	13
β-strand	390-393	4	14
β-strand	397-401	5	14
β-strand	404-406	3	13
β-strand	412-414	3	13
β-strand	417-422	6	14
β-strand	427-434	8	14
β-strand	441-446	6	15
β-strand	449-454	6	15
β-strand	458-463	6	15
β-strand	468-473	6	15
α-helix	474-475	2
α-helix	476-478	3
β-strand	485-490	6	16
β-strand	493-498	6	16
β-strand	500	1	10
α-helix	501-502	2
β-strand	508-512	5	16
β-strand	517-521	5	16
β-strand	528-531	4	10
β-strand	535	1	9

Chain D: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-19	4
β-strand	31-34	4	1
α-helix	42-56	15
α-helix	60-69	10
α-helix	75-78	4
α-helix	81-83	3
α-helix	93-106	14
α-helix	110-116	7
α-helix	122-127	6

Chain E: 20 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	24-25	2
β-strand	26	1	15
β-strand	30	1	7
β-strand	34-38	5	7
α-helix	42-51	10
α-helix	52-57	6
β-strand	63-67	5	17
β-strand	70-74	5	17
α-helix	76-82	7
α-helix	84-91	8
β-strand	101-103	3	17
α-helix	109-121	13
β-strand	123-127	5	5
α-helix	131-140	10
α-helix	144-156	13
α-helix	160-162	3
α-helix	163-172	10
α-helix	176-188	13
α-helix	190-194	5
α-helix	197-200	4
α-helix	204-212	9
β-strand	215-216	2	18
α-helix	217-219	3
α-helix	221-231	11
α-helix	233-236	4
α-helix	240-246	7
β-strand	249-250	2	18
β-strand	255-261	7	19
β-strand	268-275	8	19
β-strand	281-289	9	19
β-strand	293-299	7	20
β-strand	302-309	8	20
β-strand	312-316	5	20
β-strand	336-337	2	21
β-strand	340-344	5	22
β-strand	349-353	5	22
β-strand	356-357	2	21
β-strand	362	1	21
β-strand	366-370	5	22
β-strand	375-379	5	22
α-helix	380-382	3
β-strand	386-387	2	23
β-strand	390-393	4	24
β-strand	397-401	5	24
β-strand	404-407	4	23
α-helix	408-410	3
β-strand	411-414	4	23
β-strand	418-422	5	24
β-strand	427-430	4	24
β-strand	442-445	4	25
β-strand	450-453	4	25
β-strand	458-463	6	25
β-strand	468-473	6	25
β-strand	485-490	6	26
β-strand	493-498	6	26
β-strand	500	1	19
β-strand	502	1	27
β-strand	505	1	27
β-strand	508-512	5	26
β-strand	517-520	4	26
β-strand	530-535	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 2	A	protein	487	Homo sapiens	Q92769 (AlphaFold model)
Kelch repeat and BTB domain-containing protein 4	B, E	protein	520	Homo sapiens	Q9NVX7 (AlphaFold model)
REST corepressor 1	D	protein	401	Homo sapiens	Q9UKL0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9DTQ_1 Histone deacetylase 2 (chains A)
AYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAT
AEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAG
AVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG
DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQI
FKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGG
GGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYME
KIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEF
SDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTK
SEQLSNP

Sequence of entity 2 (B, E), FASTA

>9DTQ_2 Kelch repeat and BTB domain-containing protein 4 (chains B, E)
MESPEEPGASMDENYFVNYTFKDRSHSGRVAQGIMKLCLEEELFADVTISVEGREFQLHR
LVLSAQSCFFRSMFTSNLKEAHNRVIVLQDVSESVFQLLVDYIYHGTVKLRAEELQEIYE
VSDMYQLTSLFEECSRFLARTVQVGNCLQVMWLADRHSDPELYTAAKHCAKTHLAQLQNT
EEFLHLPHRLLTDIISDGVPCSQNPTEAIEAWINFNKEEREAFAESLRTSLKEIGENVHI
YLIGKESSRTHSLAVSLHCAEDDSISVSGQNSLCHQITAACKHGGDLYVVGGSIPRPRRM
WKCNNATVDWEWCAPLPRDRLQHTLVSVPGKDAIYSLGGKTLQDTLSNAVIYYRVGDNVW
TETTQLEVAVSGAAGANLNGIIYLLGGEENDLDFFTKPSRLIQCFDTETDKCHVKPYVLP
FAGRMHAAVHKDLVFIVAEGDSLVCYNPLLDSFTRLCLPEAWSSAPSLWKIASCNGSIYV
FRDRYKKGDANTYKLDPATSAVTVTRGIKVLLTNLQFVLA

Sequence of entity 3 (D), FASTA

>9DTQ_3 REST corepressor 1 (chains D)
MSWEEGSSGSSSDEEHGGGGMRVGPQYQAVVPDFDPAKLARRSQERDNLGMLVWSPNQNL
SEAKLDEYIAIAKEKHGYNMEQALGMLFWHKHNIEKSLADLPNFTPFPDEWTVEDKVLFE
QAFSFHGKTFHRIQQMLPDKSIASLVKFYYSWKKTRTKTSVMDRHARKQKREREESEDEL
EEANGNNPIDIEVDQNKESKKEVPPTETVPQVKKEKHSTQAKNRAKRKPPKGMFLSQEDV
EAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNA
RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAEH
GKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVRYASAS

Ligands and cofactors

ID	Name	Formula	Copies
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 Q92769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KBG 1.26 Å, Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20)
6WBZ 1.32 Å, Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a…
6WBW 1.46 Å, Structure of Human HDAC2 in complex with an ethyl ketone inhibitor
7LTL 1.49 Å, Structure of human HDAC2 in complex with an inhibitor lacking a zinc binding group…
6XEB 1.5 Å, Structure of human HDAC2 in complex with ketone inhibitor (compound E)
7ZZP 1.52 Å, Structure of HDAC2 complexed with an inhibitory ligand
6WHN 1.54 Å, Histone deacetylases complex with peptide macrocycles
7MOT 1.54 Å, Structure of HDAC2 in complex with an inhibitor (compound 9)
7MOZ 1.54 Å, Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25)
6XDM 1.56 Å, Structure of human HDAC2 in complex with an aryl ketone inhibitor
7ZZT 1.56 Å, Ligand binding to HDAC2
4LY1 1.57 Å, Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen…

Browse structure collections

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