4JJN: Heterochromatin protein Sir3

Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome. Determined by X-ray diffraction at 3.09 Å resolution. Released 15 May 2013.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Saccharomyces cerevisiae
Chains: 12
Atoms: 15,621
Mol. weight: 287.14 kDa
Released: 15 May 2013

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

Secondary structure: helices and β-sheets

4JJN contains 52 α-helices and 43 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	65-76	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chains B and F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
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	96-98	3	3

Chains C and G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-36	9
β-strand	43-44	2	4
α-helix	48-73	26
β-strand	78-79	2	5
α-helix	81-88	8
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	41-48	8
β-strand	56-57	2	5
α-helix	59-86	28
β-strand	91-92	2	4
α-helix	94-104	11
α-helix	108-127	20

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-54	9
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 H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-49	9
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

Chain K: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	11
β-strand	38-43	6	11
β-strand	49-50	2	11
β-strand	55-60	6	12
β-strand	65-75	11	12
β-strand	84-91	8	12
α-helix	93-95	3
α-helix	98-101	4
α-helix	107-110	4
α-helix	116-122	7
β-strand	131-141	11	12
α-helix	143-145	3
β-strand	146-149	4	12
β-strand	151-153	3	12
α-helix	165-166	2
β-strand	170-176	7	12
β-strand	185-186	2	12
α-helix	189-198	10
α-helix	201-210	10

Chain L: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	13
β-strand	38-43	6	13
β-strand	49-50	2	13
β-strand	55-60	6	14
β-strand	65-76	12	14
β-strand	83-91	9	14
α-helix	93-95	3
α-helix	98-101	4
α-helix	107-110	4
α-helix	116-124	9
β-strand	131-141	11	14
α-helix	143-145	3
β-strand	146-149	4	14
β-strand	151-152	2	15
α-helix	155-158	4
β-strand	170-171	2	15
β-strand	172-177	6	14
β-strand	184-186	3	14
α-helix	189-198	10
α-helix	201-210	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	135	Saccharomyces cerevisiae	P61830 (AlphaFold model)
Histone H4	B, F	protein	102	Saccharomyces cerevisiae	P02309 (AlphaFold model)
Histone H2A.2	C, G	protein	131	Saccharomyces cerevisiae	P04912 (AlphaFold model)
Histone H2B.2	D, H	protein	130	Saccharomyces cerevisiae	P02294 (AlphaFold model)
Regulatory protein SIR3	K, L	protein	382	Saccharomyces cerevisiae	P06701
DNA (146-mer)	I	DNA	147
DNA (146-mer)	J	DNA	147

Sequence of entity 1 (A, E), FASTA

>4JJN_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQ
KKDIKLARRLRGERS

Sequence of entity 2 (B, F), FASTA

>4JJN_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKS
FLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>4JJN_3 Histone H2A.2 (chains C, G)
SGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLA
AEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKK
SAKTAKASQEL

Sequence of entity 4 (D, H), FASTA

>4JJN_4 Histone H2B.2 (chains D, H)
SSAAEKKPASKAPAEKKPAAKKTSTSVDGKKRSKVRKETYSSYIYKVLKQTHPDTGISQK
SMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRA
VTKYSSSTQA

Sequence of entity 5 (K, L), FASTA

>4JJN_5 Regulatory protein SIR3 (chains K, L)
SAKTLKDLDGWQVIITDDQGRVIDDNNRRRSRKRGGENVFLKRISDGLSFGKGESVIFND
NVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYK
DKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPT
AEKFVPIDIFQIIRRVKEMEPKQSNEYLKRVSVPVSGQKTNRQVMHKMGVERSSKRLAKK
PSMKKIKIEPSADDDVNNGNIPSQRGTSTTHGSISPQEESVSPNISSASPSALTSPTDSS
KILQKRSISKELIVSEEIPINSSEQESDYEPNNETSVLSSKPGSKPEKTSTELVDGRENF
VYANNPEVSDDGGLEEETDEVS

Sequence of entity 6 (I), FASTA

>4JJN_6 DNA (146-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 7 (J), FASTA

>4JJN_7 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Primary citation

Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Wang, F., Li, G., Altaf, M. et al. Proc Natl Acad Sci U S A (2013) 110:8495-8500. DOI 10.1073/pnas.1300126110 · 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

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