6Z2J: Histone deacetylase 1

The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex. Determined by electron microscopy at 4.0 Å resolution. Released 8 Jul 2020.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,603
Mol. weight: 180.32 kDa
Ligands: ZN, IHP
Released: 8 Jul 2020

Explore 6Z2J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z2J contains 58 α-helices and 34 β-strands across 6 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: 3 helices, 0 β-strands

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

Chain B: 3 helices, 0 β-strands

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

Chain C: 17 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	1
α-helix	18-21	4
α-helix	34-44	11
α-helix	47-50	4
β-strand	52-56	5	1
α-helix	57-60	4
α-helix	61-65	5
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	200	1	3
α-helix	217-219	3
β-strand	228	1	3
β-strand	233	1	4
α-helix	234-252	19
β-strand	256-260	5	1
α-helix	263-265	3
β-strand	266	1	5
β-strand	275	1	4
β-strand	276	1	5
α-helix	278-289	12
β-strand	297-298	2	1
α-helix	305-318	14
β-strand	327	1	6
α-helix	334-336	3
β-strand	342	1	6
α-helix	356-370	15

Chains D and F: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	725-727	3
β-strand	749-753	5	1
α-helix	766-776	11
α-helix	789-798	10
α-helix	803-809	7
α-helix	823-826	4
α-helix	835-848	14
α-helix	854-858	5
α-helix	864-873	10
α-helix	876-878	3

Chain E: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	7
α-helix	18-21	4
α-helix	34-44	11
α-helix	47-50	4
β-strand	52-56	5	7
α-helix	57-60	4
α-helix	61-65	5
α-helix	70-78	9
α-helix	88-93	6
α-helix	106-125	20
β-strand	131-134	4	7
β-strand	148	1	8
β-strand	151	1	8
α-helix	155-166	12
β-strand	170-174	5	7
α-helix	181-185	5
β-strand	193-195	3	7
β-strand	200	1	9
α-helix	217-219	3
β-strand	228	1	9
β-strand	233	1	10
α-helix	234-252	19
β-strand	256-260	5	7
α-helix	263-265	3
β-strand	266	1	11
β-strand	275	1	10
β-strand	276	1	11
α-helix	278-289	12
β-strand	297-298	2	7
α-helix	305-318	14
α-helix	334-336	3
α-helix	356-370	15

Molecules and chains

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

Sequence of entity 1 (C, E), FASTA

>6Z2J_1 Histone deacetylase 1 (chains C, E)
MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN
AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS
AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG
DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI
FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG
GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE
KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF
SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK
LA

Sequence of entity 2 (A, B), FASTA

>6Z2J_2 Deoxynucleotidyltransferase terminal-interacting protein 1 (chains A, B)
MGATGDAEQPRGPSGAERGGLELGDAGAAGQLVLTNPWNIMIKHRQVQRRGRRSQMTTSF
TDPAISMDLLRAVLQPSINEEIQTVFNKYMKFFQKAALNVRDNVGEEVDAEQLIQEACRS
CLEQAKLLFS

Sequence of entity 3 (D, F), FASTA

>6Z2J_3 Mitotic deacetylase-associated SANT domain protein (chains D, F)
GAVSIEPRINVGSRFQAEIPLMRDRALAAADPHKADLVWQPWEDLESSREKQRQVEDLLT
AACSSIFPGAGTNQELALHCLHESRGDILETLNKLLLKKPLRPHNHPLATYHYTGSDQWK
MAERKLFNKGIAIYKKDFFLVQKLIQTKTVAQCVEFYYTYKKQVKIGRNGTLT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	2

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…
6Z2K 4.5 Å, The structure of the tetrameric 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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