8iht

Rpd3S bound to the nucleosome

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

Histone H3

Xenopus laevis

UniProt A0A310TTQ1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 14 DNA 2 Histone H4 × 2 (A0A8J1LTD2) Histone H2A × 2 (Q6AZJ8) Histone H2B × 2 (A0A8J0U496) DNA (164-MER) × 1 DNA (165-MER) × 1 RCO1 isoform 1 × 2 (A0A8H4BXB0) Chromatin modification-related protein EAF3 × 2 (A0A8H4F719) Transcriptional regulatory protein SIN3 × 1 (P22579) Histone deacetylase RPD3 × 1 (P32561) ZINC ION × 1 CALCIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A310TTQ1_XENLA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–135; UniProt 2–136 Author chain E; PDBConstruct 1–135; UniProt 2–136

Histone H4

Xenopus laevis

UniProt A0A8J1LTD2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 14 DNA 2 Histone H3 × 2 (A0A310TTQ1) Histone H2A × 2 (Q6AZJ8) Histone H2B × 2 (A0A8J0U496) DNA (164-MER) × 1 DNA (165-MER) × 1 RCO1 isoform 1 × 2 (A0A8H4BXB0) Chromatin modification-related protein EAF3 × 2 (A0A8H4F719) Transcriptional regulatory protein SIN3 × 1 (P22579) Histone deacetylase RPD3 × 1 (P32561) ZINC ION × 1 CALCIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A8J1LTD2_XENLA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–102; UniProt 15–116 Author chain F; PDBConstruct 1–102; UniProt 15–116

Histone H2A

Xenopus laevis

UniProt Q6AZJ8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 14 DNA 2 Histone H3 × 2 (A0A310TTQ1) Histone H4 × 2 (A0A8J1LTD2) Histone H2B × 2 (A0A8J0U496) DNA (164-MER) × 1 DNA (165-MER) × 1 RCO1 isoform 1 × 2 (A0A8H4BXB0) Chromatin modification-related protein EAF3 × 2 (A0A8H4F719) Transcriptional regulatory protein SIN3 × 1 (P22579) Histone deacetylase RPD3 × 1 (P32561) ZINC ION × 1 CALCIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q6AZJ8_XENLA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–129; UniProt 2–130 Author chain G; PDBConstruct 1–129; UniProt 2–130

Histone H2B

Xenopus laevis

UniProt A0A8J0U496

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 14 DNA 2 Histone H3 × 2 (A0A310TTQ1) Histone H4 × 2 (A0A8J1LTD2) Histone H2A × 2 (Q6AZJ8) DNA (164-MER) × 1 DNA (165-MER) × 1 RCO1 isoform 1 × 2 (A0A8H4BXB0) Chromatin modification-related protein EAF3 × 2 (A0A8H4F719) Transcriptional regulatory protein SIN3 × 1 (P22579) Histone deacetylase RPD3 × 1 (P32561) ZINC ION × 1 CALCIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A8J0U496_XENLA
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–122; UniProt 5–126 Author chain H; PDBConstruct 1–122; UniProt 5–126

RCO1 isoform 1

OrganismNot specified

UniProt A0A8H4BXB0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 14 DNA 2 Histone H3 × 2 (A0A310TTQ1) Histone H4 × 2 (A0A8J1LTD2) Histone H2A × 2 (Q6AZJ8) Histone H2B × 2 (A0A8J0U496) DNA (164-MER) × 1 DNA (165-MER) × 1 Chromatin modification-related protein EAF3 × 2 (A0A8H4F719) Transcriptional regulatory protein SIN3 × 1 (P22579) Histone deacetylase RPD3 × 1 (P32561) ZINC ION × 1 CALCIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A8H4BXB0_YEASX
Isoform —
PDB entities 7
Chains and sequence ranges Author chain M; PDBConstruct 1–684; UniProt 1–684 Author chain O; PDBConstruct 1–684; UniProt 1–684

Chromatin modification-related protein EAF3

OrganismNot specified

UniProt A0A8H4F719

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 14 DNA 2 Histone H3 × 2 (A0A310TTQ1) Histone H4 × 2 (A0A8J1LTD2) Histone H2A × 2 (Q6AZJ8) Histone H2B × 2 (A0A8J0U496) DNA (164-MER) × 1 DNA (165-MER) × 1 RCO1 isoform 1 × 2 (A0A8H4BXB0) Transcriptional regulatory protein SIN3 × 1 (P22579) Histone deacetylase RPD3 × 1 (P32561) ZINC ION × 1 CALCIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A8H4F719_YEASX
Isoform —
PDB entities 8
Chains and sequence ranges Author chain N; PDBConstruct 1–401; UniProt 1–401 Author chain P; PDBConstruct 1–401; UniProt 1–401

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 14 DNA 2 Histone H3 × 2 (A0A310TTQ1) Histone H4 × 2 (A0A8J1LTD2) Histone H2A × 2 (Q6AZJ8) Histone H2B × 2 (A0A8J0U496) DNA (164-MER) × 1 DNA (165-MER) × 1 RCO1 isoform 1 × 2 (A0A8H4BXB0) Chromatin modification-related protein EAF3 × 2 (A0A8H4F719) Histone deacetylase RPD3 × 1 (P32561) ZINC ION × 1 CALCIUM 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 9
Chains and sequence ranges Author chain K; PDBConstruct 1–1536; UniProt 1–1536

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 14 DNA 2 Histone H3 × 2 (A0A310TTQ1) Histone H4 × 2 (A0A8J1LTD2) Histone H2A × 2 (Q6AZJ8) Histone H2B × 2 (A0A8J0U496) DNA (164-MER) × 1 DNA (165-MER) × 1 RCO1 isoform 1 × 2 (A0A8H4BXB0) Chromatin modification-related protein EAF3 × 2 (A0A8H4F719) Transcriptional regulatory protein SIN3 × 1 (P22579) ZINC ION × 1 CALCIUM 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 10
Chains and sequence ranges Author chain L; PDBConstruct 1–433; UniProt 1–433

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_id8iht
Deposition date deposition_date2023-02-23
Structure title titleRpd3S bound to the nucleosome
Keywords keywordsHDAC, TRANSCRIPTION; TRANSCRIPTION
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.

8iht__assembly_1__model_1

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

Download this curve (.dat)

8iht__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.

8iht__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)57.25 Å
Rg (electron density)56.98 Å
Total Rg57.13 Å
Atom count27545
Residues3110
Excluded volume466680 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8iht__assembly_1__model_1 hexadecameric (16) 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)