4A69: HDAC3

Structure of HDAC3 bound to corepressor and inositol tetraphosphate. Determined by X-ray diffraction at 2.06 Å resolution. Released 11 Jan 2012.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 7,536
Mol. weight: 110.23 kDa
Ligands: ZN, I0P
Released: 11 Jan 2012

Explore 4A69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4A69 contains 42 α-helices and 40 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: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
α-helix	27-38	12
α-helix	41-44	4
β-strand	46-48	3	1
α-helix	55-58	4
α-helix	64-72	9
α-helix	78-81	4
α-helix	82-88	7
α-helix	100-119	20
β-strand	125-128	4	1
β-strand	137	1	2
β-strand	140	1	2
β-strand	142	1	3
β-strand	145	1	3
α-helix	149-157	9
β-strand	164-168	5	1
α-helix	175-180	6
β-strand	187-194	8	1
α-helix	212-214	3
β-strand	218-223	6	1
β-strand	228	1	4
α-helix	229-247	19
β-strand	251-255	5	1
α-helix	258-260	3
β-strand	261	1	5
β-strand	270	1	4
β-strand	271	1	5
α-helix	273-284	12
β-strand	290-293	4	1
α-helix	300-314	15
β-strand	322	1	6
α-helix	323-325	3
α-helix	329-332	4
β-strand	337	1	6
α-helix	352-367	16

Chain B: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	7
α-helix	28-38	11
α-helix	41-44	4
β-strand	46-48	3	7
α-helix	55-58	4
α-helix	64-72	9
α-helix	78-80	3
α-helix	82-88	7
α-helix	100-119	20
β-strand	125-128	4	7
β-strand	142	1	8
β-strand	145	1	8
α-helix	149-157	9
β-strand	164-168	5	7
α-helix	175-180	6
β-strand	187-194	8	7
α-helix	212-214	3
β-strand	218-223	6	7
β-strand	228	1	9
α-helix	229-247	19
β-strand	251-255	5	7
α-helix	258-260	3
β-strand	261	1	10
β-strand	270	1	9
β-strand	271	1	10
α-helix	273-285	13
β-strand	290-293	4	7
α-helix	300-314	15
β-strand	322	1	11
α-helix	323-325	3
α-helix	329-332	4
β-strand	337	1	11
α-helix	352-369	18

Chains C and D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	410	1	12
β-strand	415	1	1
β-strand	416	1	12
α-helix	419-428	10
α-helix	434-446	13
α-helix	451-456	6
α-helix	463-473	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 3,	A, B	protein	376	HOMO SAPIENS	O15379 (AlphaFold model)
Nuclear receptor corepressor 2	C, D	protein	94	HOMO SAPIENS	Q9Y618 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4A69_1 HISTONE DEACETYLASE 3, (chains A, B)
MAKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCR
FHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNN
KICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEA
FYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVI
NQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTV
RNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQ
TIFENLKMLNHAPSVQ

Sequence of entity 2 (C, D), FASTA

>4A69_2 NUCLEAR RECEPTOR COREPRESSOR 2 (chains C, D)
GAMRQLAVIPPMLYDADQQRIKFINMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQ
HPKNFGLIASFLERKTVAECVLYYYLTKKNENYK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
I0P	D-myo inositol 1,4,5,6 tetrakisphosphate	C6 H16 O18 P4	2

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

Primary citation

Structure of Hdac3 Bound to Co-Repressor and Inositol Tetraphosphate. Watson, P.J., Fairall, L., Santos, G.M. et al. Nature (2012) 481:335. DOI 10.1038/NATURE10728 · PubMed

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