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8vlr

Cryo-EM structure of native H2AK119bu nucleosome at 2.6

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

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 8 DNA 2 Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-A × 2 （Q96A08） DNA (136-MER) × 1 DNA (136-MER) × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2b2t 2b2u 2b2v 2b2w 2cv5 2l75 2ri7 2uxn 3a1b 3afa 3ayw 3aze

476 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name H31_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–98； UniProt 39–136 Author chain E； PDBConstruct 1–98； UniProt 39–136

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 8 DNA 2 Histone H3.1 × 2 （P68431） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-A × 2 （Q96A08） DNA (136-MER) × 1 DNA (136-MER) × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
10xz 10ya 10yb 10yc 10yd 10ye 10yf 10yg 10yh 10yi 2bqz 2bqz

634 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name H4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–84； UniProt 20–103 Author chain F； PDBConstruct 1–84； UniProt 20–103

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 8 DNA 2 Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 1-A × 2 （Q96A08） DNA (136-MER) × 1 DNA (136-MER) × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2rvq 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi

351 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name H2A1B_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–108； UniProt 12–119 Author chain G； PDBConstruct 1–108； UniProt 12–119

Histone H2B type 1-A

OrganismNot specified

UniProt Q96A08

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 2 Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） DNA (136-MER) × 1 DNA (136-MER) × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3wkj 5gsu 5gt3 8vlr

4 assemblies

View Construct and Data Evidence
UniProt name H2B1A_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–93； UniProt 34–126 Author chain H； PDBConstruct 1–93； UniProt 34–126

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_id8vlr
Deposition date deposition_date2024-01-12
Last revision last_revision2025-01-15
Structure title titleCryo-EM structure of native H2AK119bu nucleosome at 2.6
Keywords keywordsNucleosome, native H2AK119bu, cryo-EM, 2.6, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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.

8vlr__assembly_1__model_1

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

Download this curve (.dat)

8vlr__assembly_1__model_1 | I(q)

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

8vlr__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）39.10 Å
Rg (electron density)36.38 Å
Total Rg37.12 Å
Atom count21181
Residues1038
Excluded volume190630 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8vlr__assembly_1__model_1 decameric （10） 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 (6)

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7. Citations (1)