1ID3: Histone H3

Crystal structure of the yeast nucleosome core particle reveals fundamental differences in inter-nucleosome interactions. Determined by X-ray diffraction at 3.1 Å resolution. Released 28 Sept 2001.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 10
Atoms: 12,124
Mol. weight: 200.15 kDa
Ligands: MN
Released: 28 Sept 2001

Explore 1ID3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ID3 contains 38 α-helices and 20 β-strands across 8 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-129	9

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	28-36	9
β-strand	43-44	2	4
α-helix	48-73	26
β-strand	78-79	2	5
α-helix	81-89	9
α-helix	92-97	6
β-strand	101-103	3	6
α-helix	114-116	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	5
α-helix	59-86	28
β-strand	91-92	2	4
α-helix	94-104	11
α-helix	107-126	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-76	27
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-37	10
β-strand	43-44	2	9
α-helix	48-73	26
β-strand	78-79	2	10
α-helix	81-90	10
α-helix	92-97	6
β-strand	102-103	2	3
α-helix	114-116	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-51	11
β-strand	56-57	2	10
α-helix	59-86	28
β-strand	91-92	2	9
α-helix	94-104	11
α-helix	107-122	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Palindromic 146BP DNA fragment	I, J	DNA	146	Homo sapiens
Histone H3	A, E	protein	135	Saccharomyces cerevisiae	P61830 (AlphaFold model)
Histone H4	B, F	protein	102	Saccharomyces cerevisiae	P02309 (AlphaFold model)
Histone H2A.1	C, G	protein	131	Saccharomyces cerevisiae	P04911 (AlphaFold model)
Histone H2B.2	D, H	protein	130	Saccharomyces cerevisiae	P02294 (AlphaFold model)

Sequence of entity 1 (I, J), FASTA

>1ID3_1 PALINDROMIC 146BP DNA FRAGMENT (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 2 (A, E), FASTA

>1ID3_2 HISTONE H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQ
KKEIKLARRLRGERS

Sequence of entity 3 (B, F), FASTA

>1ID3_3 HISTONE H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKS
FLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>1ID3_4 HISTONE H2A.1 (chains C, G)
SGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLA
AEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK
SAKATKASQEL

Sequence of entity 5 (D, H), FASTA

>1ID3_5 HISTONE H2B.2 (chains D, H)
SSAAEKKPASKAPAEKKPAAKKTSTSVDGKKRSKVRKETYSSYIYKVLKQTHPDTGISQK
SMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRA
VTKYSSSTQA

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	17

Primary citation

Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. White, C.L., Suto, R.K., Luger, K. EMBO J (2001) 20:5207-5218. DOI 10.1093/emboj/20.18.5207 · PubMed

Other PDB entries of the same protein (UniProt P61830 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KMJ 1.4 Å, Crystal structure of Sth1 bromodomain in complex with H3K14Ac
7F3S 1.4 Å, Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
8I3F 1.62 Å, Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
7F4E 1.78 Å, Crystal structure of Hst2 in complex with H3K9bz peptide
5D7E 1.9 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9ac
7F4A 2.0 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
1M1D 2.2 Å, Tetrahymena GCN5 with bound bisubstrate analog inhibitor
1QSN 2.2 Å, Crystal structure of tetrahymena GCN5 with bound coenzyme a and histone H3 peptide
2IDC 2.2 Å, Structure of the Histone H3-Asf1 Chaperone Interaction
5IOK 2.22 Å, Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr

Browse structure collections

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