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8HY0

Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, E
(A, E)
Histone H3polymer13515332.02UniProt (A0A310TTQ1)
Pfam (PF00125)
UniProt (by SIFTS) (P84233)
Xenopus laevis (African clawed frog)
2B, F
(B, F)
Histone H4polymer10211263.22UniProt (A0A8J1LTD2)
Pfam (PF15511)
UniProt (by SIFTS) (P62799)
Xenopus laevis (African clawed frog)
3C, G
(C, G)
Histone H2Apolymer12913978.22UniProt (Q6AZJ8)
Pfam (PF00125)
Pfam (PF16211)
UniProt (by SIFTS) (P06897)
Xenopus laevis (African clawed frog)
4D, H
(D, H)
Histone H2Bpolymer12213524.82UniProt (A0A8J0U496)
Pfam (PF00125)
UniProt (by SIFTS) (P02281)
Xenopus laevis (African clawed frog)
5I
(I)
DNA (352-MER)polymer352108340.81synthetic construct
6J
(J)
DNA (352-MER)polymer352109079.31synthetic construct
7K
(K)
Transcriptional regulatory protein SIN3polymer1536175047.31UniProt (P22579)
Pfam (PF16879)
Pfam (PF02671)
Pfam (PF08295)
Saccharomyces cerevisiae (baker's yeast)
8L
(L)
Histone deacetylase RPD3polymer43348962.01UniProt (P32561)
Pfam (PF00850)
Saccharomyces cerevisiae (baker's yeast)Transcriptional regulatory protein RPD3
9M, O
(M, O)
Chromatin modification-related protein EAF3polymer40145266.42UniProt (A0A8H4F719)
Pfam (PF11717)
Pfam (PF22732)
Pfam (PF05712)
UniProt (by SIFTS) (Q12432)
Saccharomyces cerevisiae (baker's yeast)
10N, P
(N, P)
RCO1 isoform 1polymer68478951.32UniProt (A0A8H4BXB0)
Pfam (PF00628)
UniProt (by SIFTS) (Q04779)
Saccharomyces cerevisiae (baker's yeast)
11Q, R, S, T, U...
(L, N, P)
ZINC IONnon-polymer65.47Chemie (ZN)
Sequence modifications
A, E: 1 - 135 (UniProt: A0A310TTQ1)
PDBExternal DatabaseDetails
Ala 110Cys 111engineered mutation
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains16
Total formula weight798061.2
Non-Polymers*Number of molecules7
Total formula weight457.9
All*Total formula weight798519.0
*Water molecules are not included.

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PDB entries from 2024-11-06

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