4KUD: Histone H3

Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle. Determined by X-ray diffraction at 3.2 Å resolution. Released 7 Aug 2013.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 12
Atoms: 15,732
Mol. weight: 253.78 kDa
Released: 7 Aug 2013

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

Secondary structure: helices and β-sheets

4KUD contains 55 α-helices and 46 β-strands across 10 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	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-37	10
β-strand	43-44	2	4
α-helix	48-72	25
β-strand	78-79	2	5
α-helix	81-90	10
α-helix	92-97	6
β-strand	101-103	3	6

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	107-127	21

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-36	9
β-strand	43-44	2	9
α-helix	48-72	25
β-strand	78-79	2	10
α-helix	81-90	10
α-helix	92-97	6
β-strand	101-103	3	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	107-126	20

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	136	Saccharomyces cerevisiae	P61830 (AlphaFold model)
Histone H4	B, F	protein	103	Saccharomyces cerevisiae	P02309 (AlphaFold model)
Histone H2A.2	C, G	protein	132	Saccharomyces cerevisiae	P04912 (AlphaFold model)
Histone H2B.1	D, H	protein	131	Saccharomyces cerevisiae	P02293 (AlphaFold model)
nucloesome DNA	I, J	DNA	146
Regulatory protein SIR3	K, L	protein	224	Saccharomyces cerevisiae	P06701

Sequence of entity 1 (A, E), FASTA

>4KUD_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS

Sequence of entity 2 (B, F), FASTA

>4KUD_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>4KUD_3 Histone H2A.2 (chains C, G)
MAGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKTAKASQEL

Sequence of entity 4 (D, H), FASTA

>4KUD_4 Histone H2B.1 (chains D, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA

Sequence of entity 5 (I, J), FASTA

>4KUD_5 nucloesome DNA (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 6 (K, L), FASTA

>4KUD_6 Regulatory protein SIR3 (chains K, L)
AKTLKDLDGWQVIITDDQGRVIDDNNRRRSRKRGGENVFLKRISDGLSFGKGESVIFNDN
VTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKD
KFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTA
EKFVPIDIFQIIRRVKEMEPKQSNEYLKRVSVPVSGQKHHHHHH

Primary citation

N alpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain. Yang, D., Fang, Q., Wang, M. et al. Nat Struct Mol Biol (2013) 20:1116-1118. DOI 10.1038/nsmb.2637 · 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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