6Z2K: Histone deacetylase 1

The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex. Determined by electron microscopy at 4.5 Å resolution. Released 8 Jul 2020.

Method: Electron microscopy
Resolution: 4.5 Å
Organism: Homo sapiens
Chains: 12
Atoms: 19,266
Mol. weight: 360.63 kDa
Ligands: ZN, IHP
Released: 8 Jul 2020

Explore 6Z2K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z2K contains 104 α-helices and 66 β-strands across 12 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.

Chains A and G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	65-103	39
α-helix	110-125	16
α-helix	126-129	4

Chains B and H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	63-104	42
α-helix	110-125	16
α-helix	126-129	4

Chains C, I and K: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	1
α-helix	17-20	4
α-helix	33-44	12
α-helix	48-50	3
β-strand	52-56	5	1
α-helix	57-60	4
α-helix	61-64	4
α-helix	70-78	9
α-helix	88-93	6
α-helix	106-125	20
β-strand	131-134	4	1
β-strand	148	1	2
β-strand	151	1	2
α-helix	155-166	12
β-strand	170-174	5	1
α-helix	181-185	5
β-strand	193-195	3	1
β-strand	198-200	3	3
α-helix	217-219	3
β-strand	223	1	1
β-strand	226-228	3	3
α-helix	234-251	18
β-strand	256-260	5	1
β-strand	266	1	4
β-strand	276	1	4
α-helix	278-290	13
β-strand	295-298	4	1
α-helix	305-319	15
β-strand	327	1	5
α-helix	334-336	3
β-strand	342	1	5
α-helix	356-371	16

Chain D: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	749-751	3	1
α-helix	766-774	9
α-helix	787-798	12
α-helix	803-810	8
α-helix	823-828	6
α-helix	835-847	13
α-helix	854-858	5
α-helix	864-878	15

Chain E: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	6
α-helix	17-20	4
α-helix	33-44	12
α-helix	48-50	3
β-strand	52-56	5	6
α-helix	57-60	4
α-helix	61-64	4
α-helix	70-78	9
α-helix	88-93	6
α-helix	106-125	20
β-strand	131-134	4	6
β-strand	148	1	7
β-strand	151	1	7
α-helix	155-166	12
β-strand	170-174	5	6
α-helix	181-185	5
β-strand	193-195	3	6
β-strand	198-200	3	8
α-helix	217-219	3
β-strand	223	1	6
β-strand	226-228	3	8
α-helix	234-251	18
β-strand	256-260	5	6
β-strand	266	1	9
β-strand	276	1	9
α-helix	278-290	13
β-strand	295-298	4	6
α-helix	305-319	15
α-helix	334-336	3
α-helix	356-371	16

Chains F, J and L: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	749-753	5	6
α-helix	766-774	9
α-helix	787-798	12
α-helix	803-810	8
α-helix	823-828	6
α-helix	835-847	13
α-helix	854-858	5
α-helix	864-878	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 1	C, E, I, K	protein	482	Homo sapiens	Q13547 (AlphaFold model)
Deoxynucleotidyltransferase terminal-interacting protein 1	A, B, G, H	protein	130	Homo sapiens	Q9H147 (AlphaFold model)
Mitotic deacetylase-associated SANT domain protein	D, F, J, L	protein	173	Homo sapiens	Q6PJG2 (AlphaFold model)

Sequence of entity 1 (C, E, I, K), FASTA

>6Z2K_1 Histone deacetylase 1 (chains C, E, I, K)
MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN
AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS
AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG
DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI
FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG
GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE
KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF
SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK
LA

Sequence of entity 2 (A, B, G, H), FASTA

>6Z2K_2 Deoxynucleotidyltransferase terminal-interacting protein 1 (chains A, B, G, H)
MGATGDAEQPRGPSGAERGGLELGDAGAAGQLVLTNPWNIMIKHRQVQRRGRRSQMTTSF
TDPAISMDLLRAVLQPSINEEIQTVFNKYMKFFQKAALNVRDNVGEEVDAEQLIQEACRS
CLEQAKLLFS

Sequence of entity 3 (D, F, J, L), FASTA

>6Z2K_3 Mitotic deacetylase-associated SANT domain protein (chains D, F, J, L)
GAVSIEPRINVGSRFQAEIPLMRDRALAAADPHKADLVWQPWEDLESSREKQRQVEDLLT
AACSSIFPGAGTNQELALHCLHESRGDILETLNKLLLKKPLRPHNHPLATYHYTGSDQWK
MAERKLFNKGIAIYKKDFFLVQKLIQTKTVAQCVEFYYTYKKQVKIGRNGTLT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	4

Water and common crystallization additives (K) are not listed.

Primary citation

The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Turnbull, R.E., Fairall, L., Saleh, A. et al. Nat Commun (2020) 11:3252-3252. DOI 10.1038/s41467-020-17078-8 · PubMed

Other PDB entries of the same protein (UniProt Q13547 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SME 2.64 Å, p107 pocket domain complexed with HDAC1 peptide
9R4I 2.92 Å, An auto inhibitory loop in the MiDAC histone deacetylase complex
4BKX 3.0 Å, The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the…
5ICN 3.3 Å, HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on…
8VPQ 3.3 Å, The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML
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…
6Z2J 4.0 Å, The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex
7AO8 4.5 Å, Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex
7AO9 6.1 Å, Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex
7AOA 19.4 Å, Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex
9A07 Integrative Modeling of a Sin3/HDAC Complex Sub-structure

Browse structure collections

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