8KD3

Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	Histone deacetylase RPD3	polymer	433	48962.0	1	UniProt (P32561) Pfam (PF00850)	Saccharomyces cerevisiae (baker's yeast)
2	B (B)	Transcriptional regulatory protein SIN3	polymer	1544	176152.4	1	UniProt (P22579) Pfam (PF02671) Pfam (PF08295) Pfam (PF16879)	Saccharomyces cerevisiae (baker's yeast)
3	C, E (D, F)	Chromatin modification-related protein EAF3	polymer	401	45266.4	2	UniProt (Q12432) Pfam (PF11717) Pfam (PF22732) Pfam (PF05712)	Saccharomyces cerevisiae (baker's yeast)	ESA1-associated factor 3
4	D, F (E, G)	Transcriptional regulatory protein RCO1	polymer	733	84469.3	2	UniProt (Q04779) Pfam (PF00628)	Saccharomyces cerevisiae (baker's yeast)
5	G, K (O, S)	Histone H3	polymer	135	15312.9	2	UniProt (A0A310TTQ1) Pfam (PF00125)	Xenopus laevis (African clawed frog)
6	H, L (P, T)	Histone H4	polymer	102	11263.2	2	UniProt (P62799) Pfam (PF15511)	Xenopus laevis (African clawed frog)
7	I, M (Q, U)	Histone H2A	polymer	129	13978.2	2	UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211)	Xenopus laevis (African clawed frog)
8	J, N (R, V)	Histone H2B 1.1	polymer	122	13524.8	2	UniProt (P02281) Pfam (PF00125)	Xenopus laevis (African clawed frog)	H2B1.1
9	O (X)	187bp DNA	polymer	187	58077.9	1		synthetic construct
10	P (Y)	187bp DNA	polymer	187	57397.5	1		synthetic construct
11	Q (A)	ZINC ION	non-polymer		65.4	1	Chemie (ZN)

Sequence modifications

B: 2 - 1536 (UniProt: P22579)

PDB	External Database	Details
Met -7	-	initiating methionine
His -6	-	expression tag
His -5	-	expression tag
His -4	-	expression tag
His -3	-	expression tag
His -2	-	expression tag
His -1	-	expression tag
His 0	-	expression tag
His 1	-	expression tag

E, G: 1 - 684 (UniProt: Q04779)

PDB	External Database	Details
Met 685	-	expression tag
His 686	-	expression tag
His 687	-	expression tag
His 688	-	expression tag
His 689	-	expression tag
His 690	-	expression tag
His 691	-	expression tag
His 692	-	expression tag
His 693	-	expression tag
Pro 694	-	expression tag
Gln 695	-	expression tag
Leu 696	-	expression tag
Ala 697	-	expression tag
Met 698	-	expression tag
Trp 699	-	expression tag
Ser 700	-	expression tag
His 701	-	expression tag
Pro 702	-	expression tag
Gln 703	-	expression tag
Phe 704	-	expression tag
Glu 705	-	expression tag
Lys 706	-	expression tag
Gly 707	-	expression tag
Gly 708	-	expression tag
Gly 709	-	expression tag
Ser 710	-	expression tag
Gly 711	-	expression tag
Gly 712	-	expression tag
Gly 713	-	expression tag
Ser 714	-	expression tag
Gly 715	-	expression tag
Gly 716	-	expression tag
Gly 717	-	expression tag
Ser 718	-	expression tag
Trp 719	-	expression tag
Ser 720	-	expression tag
His 721	-	expression tag
Pro 722	-	expression tag
Gln 723	-	expression tag
Phe 724	-	expression tag
Glu 725	-	expression tag
Lys 726	-	expression tag
Glu 727	-	expression tag
Asn 728	-	expression tag
Leu 729	-	expression tag
Tyr 730	-	expression tag
Phe 731	-	expression tag
Gln 732	-	expression tag
Ser 733	-	expression tag

O, S: 1 - 135 (UniProt: A0A310TTQ1)

PDB	External Database	Details
Gln 9	Lys 10	engineered mutation
Ala 110	Cys 111	engineered mutation

R, V: 1 - 122 (UniProt: P02281)

PDB	External Database	Details
Thr 29	Ser 33	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	16
	Total formula weight	708219.5
Non-Polymers*	Number of molecules	1
	Total formula weight	65.4
All*	Total formula weight	708284.9

*Water molecules are not included.