ISDA: 9V2W

Deposition Date 2025-05-21

Release Date 2026-05-27

Last Version Date 2026-05-27

Entry Detail

PDB ID:

9V2W

Keywords:

GENE REGULATION/DNA

Title:

Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome

Biological Source:

Source Organism(s):

Saccharomyces cerevisiae S288C (Taxon ID: 559292)
Xenopus laevis (Taxon ID: 8355)
synthetic construct (Taxon ID: 32630)

Expression System(s):

Trichoplusia ni, Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):SIN3
Chain IDs:A
Chain Length:1096
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P22579 Pfam ID:PF02671, PF08295, PF16879

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):LOC494591
Chain IDs:B, M, O, S
Chain Length:107
Number of Molecules:4
Biological Source:Xenopus laevis

UniProt ID:Q6AZJ8 Pfam ID:PF00125, PF16211

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone deacetylase RPD3
Gene (Uniprot):RPD3
Chain IDs:C
Chain Length:378
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P32561 Pfam ID:PF00850 EC:3.5.1.98

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B
Gene (Uniprot):LOC108704302
Chain IDs:D, N, P, T
Chain Length:93
Number of Molecules:4
Biological Source:Xenopus laevis

UniProt ID:A0A8J1LZU9 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):DEP1
Chain IDs:E
Chain Length:119
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P31385 Pfam ID:PF08598

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):SDS3
Chain IDs:F
Chain Length:311
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P40505 Pfam ID:PF08598

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):SAP30
Chain IDs:G
Chain Length:119
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P38429 Pfam ID:PF13867

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3
Gene (Uniprot):LOC121398065
Chain IDs:H, Q, U, W
Chain Length:98
Number of Molecules:4
Biological Source:Xenopus laevis

UniProt ID:A0A310TTQ1 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):PHO23
Chain IDs:I
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P50947 Pfam ID:PF12998

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):RXT2
Chain IDs:J
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P38255 Pfam ID:PF08595

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone deacetylase complex s
Gene (Uniprot):CTI6
Chain IDs:K
Chain Length:249
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:Q08923

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:L, R, V, X (auth: Z)
Chain Length:79
Number of Molecules:4
Biological Source:Xenopus laevis

UniProt ID:P62799 Pfam ID:PF15511

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (329-MER)
Chain IDs:Y (auth: X)
Chain Length:329
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (329-MER)
Chain IDs:Z (auth: Y)
Chain Length:329
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

Chromatin context-dependent deacetylation by the asymmetric Rpd3L

Zhao, H, Li, H, Wang, C, Yang, X, Zou, B, Dong, S, Zhang, N, Zhou, Y, Yi, L, Zhang, Y, Xie, Y, Qin, D, Chao, W, Pei, D, He, J.Show

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