8w9e

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcriptional regulatory protein SIN3

OrganismNot specified

UniProt P22579

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein RCO1 × 2 (Q04779) Histone deacetylase RPD3 × 1 (P32561) Chromatin modification-related protein EAF3 × 3 (Q12432) Histone H3.1 × 2 (P68431) Histone H4 × 2 (P62805) Histone H2A type 1-B/E × 2 (P04908) Histone H2B type 1-K × 2 (O60814) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SIN3_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1536; UniProt 1–1536

Transcriptional regulatory protein RCO1

OrganismNot specified

UniProt Q04779

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein SIN3 × 1 (P22579) Histone deacetylase RPD3 × 1 (P32561) Chromatin modification-related protein EAF3 × 3 (Q12432) Histone H3.1 × 2 (P68431) Histone H4 × 2 (P62805) Histone H2A type 1-B/E × 2 (P04908) Histone H2B type 1-K × 2 (O60814) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RCO1_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–684; UniProt 1–684 Author chain F; PDBConstruct 1–684; UniProt 1–684

Histone deacetylase RPD3

OrganismNot specified

UniProt P32561

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein SIN3 × 1 (P22579) Transcriptional regulatory protein RCO1 × 2 (Q04779) Chromatin modification-related protein EAF3 × 3 (Q12432) Histone H3.1 × 2 (P68431) Histone H4 × 2 (P62805) Histone H2A type 1-B/E × 2 (P04908) Histone H2B type 1-K × 2 (O60814) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPD3_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 1–433; UniProt 1–433

Chromatin modification-related protein EAF3

OrganismNot specified

UniProt Q12432

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein SIN3 × 1 (P22579) Transcriptional regulatory protein RCO1 × 2 (Q04779) Histone deacetylase RPD3 × 1 (P32561) Histone H3.1 × 2 (P68431) Histone H4 × 2 (P62805) Histone H2A type 1-B/E × 2 (P04908) Histone H2B type 1-K × 2 (O60814) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name EAF3_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 1–401; UniProt 1–401 Author chain D; PDBConstruct 1–401; UniProt 1–401 Author chain G; PDBConstruct 1–401; UniProt 1–401

Histone H3.1

OrganismNot specified

UniProt P68431

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein SIN3 × 1 (P22579) Transcriptional regulatory protein RCO1 × 2 (Q04779) Histone deacetylase RPD3 × 1 (P32561) Chromatin modification-related protein EAF3 × 3 (Q12432) Histone H4 × 2 (P62805) Histone H2A type 1-B/E × 2 (P04908) Histone H2B type 1-K × 2 (O60814) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H31_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain a; PDBConstruct 1–136; UniProt 1–136 Author chain e; PDBConstruct 1–136; UniProt 1–136

Histone H4

OrganismNot specified

UniProt P62805

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein SIN3 × 1 (P22579) Transcriptional regulatory protein RCO1 × 2 (Q04779) Histone deacetylase RPD3 × 1 (P32561) Chromatin modification-related protein EAF3 × 3 (Q12432) Histone H3.1 × 2 (P68431) Histone H2A type 1-B/E × 2 (P04908) Histone H2B type 1-K × 2 (O60814) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H4_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain b; PDBConstruct 1–103; UniProt 1–103 Author chain f; PDBConstruct 1–103; UniProt 1–103

Histone H2A type 1-B/E

OrganismNot specified

UniProt P04908

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein SIN3 × 1 (P22579) Transcriptional regulatory protein RCO1 × 2 (Q04779) Histone deacetylase RPD3 × 1 (P32561) Chromatin modification-related protein EAF3 × 3 (Q12432) Histone H3.1 × 2 (P68431) Histone H4 × 2 (P62805) Histone H2B type 1-K × 2 (O60814) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H2A1B_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain c; PDBConstruct 1–130; UniProt 1–130 Author chain g; PDBConstruct 1–130; UniProt 1–130

Histone H2B type 1-K

OrganismNot specified

UniProt O60814

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 15 DNA 2 Transcriptional regulatory protein SIN3 × 1 (P22579) Transcriptional regulatory protein RCO1 × 2 (Q04779) Histone deacetylase RPD3 × 1 (P32561) Chromatin modification-related protein EAF3 × 3 (Q12432) Histone H3.1 × 2 (P68431) Histone H4 × 2 (P62805) Histone H2A type 1-B/E × 2 (P04908) 5-DNA × 1 3-DNA × 1 ZINC ION × 7 POTASSIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H2B1K_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain d; PDBConstruct 1–126; UniProt 1–126 Author chain h; PDBConstruct 1–126; UniProt 1–126

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id8w9e
Deposition date deposition_date2023-09-05
Structure title titleCryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2
Keywords keywordsRpd3S, HDAC, Sin3, Rpd3, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8w9e__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8w9e__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8w9e__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)53.92 Å
Rg (electron density)53.15 Å
Total Rg53.44 Å
Atom count27886
Residues2991
Excluded volume479220 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8w9e__assembly_1__model_1 17-meric (17) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (12)

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7. Citations (1)