9R4I: Histone deacetylase 1

An auto inhibitory loop in the MiDAC histone deacetylase complex. Determined by electron microscopy at 2.92 Å resolution. Released 25 Feb 2026.

Method: Electron microscopy
Resolution: 2.92 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,475
Mol. weight: 244.65 kDa
Ligands: ZN, IHP
Released: 25 Feb 2026

Explore 9R4I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9R4I contains 60 α-helices and 32 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	1
α-helix	17-21	5
α-helix	33-44	12
α-helix	47-50	4
β-strand	52-56	5	1
α-helix	57-58	2
α-helix	61-64	4
α-helix	70-78	9
α-helix	88-94	7
α-helix	106-125	20
β-strand	131-134	4	1
β-strand	143	1	2
β-strand	146	1	2
α-helix	155-163	9
β-strand	170-174	5	1
α-helix	181-186	6
β-strand	193-200	8	1
β-strand	223-228	6	1
α-helix	234-251	18
β-strand	256-260	5	1
β-strand	266	1	3
β-strand	276	1	3
α-helix	278-289	12
β-strand	295-298	4	1
α-helix	305-320	16
β-strand	327	1	4
α-helix	334-336	3
β-strand	342	1	4
α-helix	356-371	16

Chain B: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	656-658	3
α-helix	731-736	6
α-helix	739-743	5
β-strand	749-753	5	1
α-helix	763-776	14
α-helix	788-797	10
α-helix	802-806	5
α-helix	807-811	5
α-helix	825-827	3
α-helix	835-848	14
α-helix	852-858	7
α-helix	864-873	10

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	5
β-strand	54	1	5
α-helix	63-104	42
α-helix	110-124	15
α-helix	127-130	4

Chain D: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	11-14	4	6
α-helix	17-21	5
α-helix	33-45	13
α-helix	47-50	4
β-strand	52-56	5	6
α-helix	61-67	7
α-helix	70-78	9
α-helix	81-83	3
α-helix	88-94	7
α-helix	106-125	20
β-strand	131-134	4	6
β-strand	143	1	7
β-strand	146	1	7
α-helix	155-164	10
β-strand	170-174	5	6
α-helix	181-186	6
β-strand	193-200	8	6
β-strand	223-228	6	6
α-helix	234-251	18
β-strand	256-260	5	6
α-helix	263-265	3
α-helix	278-289	12
β-strand	295-298	4	6
α-helix	305-320	16
β-strand	327	1	8
α-helix	334-336	3
β-strand	342	1	8
α-helix	356-371	16

Chain E: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	733-736	4
α-helix	739-743	5
β-strand	749-753	5	6
α-helix	763-775	13
α-helix	782-784	3
α-helix	788-797	10
α-helix	802-806	5
α-helix	807-811	5
α-helix	825-827	3
α-helix	835-848	14
α-helix	852-858	7
α-helix	864-873	10

Chain F: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	9
β-strand	55-56	2	9
α-helix	63-88	26
α-helix	90-104	15
α-helix	110-130	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 1	A, D	protein	482	Homo sapiens	Q13547 (AlphaFold model)
Mitotic deacetylase-associated SANT domain protein	B, E	protein	260	Homo sapiens	Q6PJG2 (AlphaFold model)
Deoxynucleotidyltransferase terminal-interacting protein 1	C, F	protein	329	Homo sapiens	Q9H147 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9R4I_1 Histone deacetylase 1 (chains A, D)
MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN
AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS
AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG
DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI
FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG
GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE
KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF
SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK
LA

Sequence of entity 2 (B, E), FASTA

>9R4I_2 Mitotic deacetylase-associated SANT domain protein (chains B, E)
TPYQSHLRSPVRLADHPSERSFELPPYTPPPILSPVREGSGLYFNAIISTSTIPAPPPIT
PKSAHRTLLRTNSAEVTPPVLSVMGEATPVSIEPRINVGSRFQAEIPLMRDRALAAADPH
KADLVWQPWEDLESSREKQRQVEDLLTAACSSIFPGAGTNQELALHCLHESRGDILETLN
KLLLKKPLRPHNHPLATYHYTGSDQWKMAERKLFNKGIAIYKKDFFLVQKLIQTKTVAQC
VEFYYTYKKQVKIGRNGTLT

Sequence of entity 3 (C, F), FASTA

>9R4I_3 Deoxynucleotidyltransferase terminal-interacting protein 1 (chains C, F)
MGATGDAEQPRGPSGAERGGLELGDAGAAGQLVLTNPWNIMIKHRQVQRRGRRSQMTTSF
TDPAISMDLLRAVLQPSINEEIQTVFNKYMKFFQKAALNVRDNVGEEVDAEQLIQEACRS
CLEQAKLLFSDGEKVIPRLTHELPGIKRGRQAEEECAHRGSPLPKKRKGRPPGHILSSDR
AAAGMVWKPKSCEPIRREGPKWDPARLNESTTFVLGSRANKALGMGGTRGRIYIKHPHLF
KYAADPQDKHWLAEQHHMRATGGKMAYLLIEEDIRDLAASDDYRGCLDLKLEELKSFVLP
SWMVEKMRKYMETLRTENEHRAVEAPPQT

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

A de novo missense variant in MIDEAS results in increased deacetylase activity of the MiDAC HDAC complex causing a neurodevelopmental syndrome. Fairall, L., Sirvydis, K., Turnbull, R.E. et al. Nat Commun (2025) 16:10472-10472. DOI 10.1038/s41467-025-65472-x · 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
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
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

About this viewer

MolViewer shows 9R4I directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.