ISDA: 9V2V

Deposition Date 2025-05-21

Release Date 2026-05-06

Last Version Date 2026-05-06

Entry Detail

PDB ID:

9V2V

Keywords:

GENE REGULATION/DNA

Title:

Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-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:

3.00 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, B
Chain Length:683
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P22579

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone deacetylase RPD3
Gene (Uniprot):RPD3
Chain IDs:C, D
Chain Length:385
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P32561 EC:3.5.1.98

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

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):SAP30
Chain IDs:G
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P38429

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):RXT3
Chain IDs:H
Chain Length:211
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:Q07458

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcriptional regulatory pr
Gene (Uniprot):RXT2
Chain IDs:J
Chain Length:218
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P38255

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone deacetylase complex s
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 H2A
Gene (Uniprot):LOC494591
Chain IDs:L (auth: O), P (auth: S)
Chain Length:107
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:Q6AZJ8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B
Gene (Uniprot):LOC108704302
Chain IDs:M (auth: P), Q (auth: T)
Chain Length:93
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:A0A8J1LZU9

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3
Gene (Uniprot):LOC121398065
Chain IDs:N (auth: Q), R (auth: U)
Chain Length:98
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:A0A310TTQ1

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:O (auth: R), S (auth: V)
Chain Length:79
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P62799

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (155-MER)
Chain IDs:T (auth: X)
Chain Length:155
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (155-MER)
Chain IDs:U (auth: Y)
Chain Length:155
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

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

Zhao, H, Li, H, Wang, C, Yang, X, Li, H, 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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