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6yn1

Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 heterocomplex Heteromer Protein 10 Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 CHLORIDE ION × 1 water × 10 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 10 Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 10 Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 water × 10 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 10 Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1s32 21vv 21wa 21wc 2nzd 3b6f 3b6g 3kuy 3kwq 3kxb 3lel 3lel

239 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q6AZJ8_XENLA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–107； UniProt 14–119 Author chain F； PDBConstruct 2–107； UniProt 14–119 Author chain K； PDBConstruct 2–107； UniProt 14–119 Author chain P； PDBConstruct 2–107； UniProt 14–119 Author chain U； PDBConstruct 2–107； UniProt 14–119 Author chain Z； PDBConstruct 2–107； UniProt 14–119 Author chain e； PDBConstruct 2–107； UniProt 14–119 Author chain j； PDBConstruct 2–107； UniProt 14–119

Histone H2B

Xenopus laevis

UniProt A0A1L8FQA5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 CHLORIDE ION × 1 water × 10 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 water × 10 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6iy2 6iy3 6yn1 6yn1 6yn1 6yn1 6z6p 7ea5 7ktq 9ear

10 assemblies

View Construct and Data Evidence
UniProt name A0A1L8FQA5_XENLA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–100； UniProt 28–126 Author chain G； PDBConstruct 2–100； UniProt 28–126 Author chain L； PDBConstruct 2–100； UniProt 28–126 Author chain Q； PDBConstruct 2–100； UniProt 28–126 Author chain V； PDBConstruct 2–100； UniProt 28–126 Author chain a； PDBConstruct 2–100； UniProt 28–126 Author chain f； PDBConstruct 2–100； UniProt 28–126 Author chain k； PDBConstruct 2–100； UniProt 28–126

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 heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 CHLORIDE ION × 1 water × 10 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 water × 10 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H4 × 2 （P62799） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1s32 21vv 21wa 21wc 6iro 6iy2 6iy3 6j99 6jyl 6k1p 6kiu 6kiv

131 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name A0A310TTQ1_XENLA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 2–99； UniProt 39–136 Author chain H； PDBConstruct 2–99； UniProt 39–136 Author chain M； PDBConstruct 2–99； UniProt 39–136 Author chain R； PDBConstruct 2–99； UniProt 39–136 Author chain W； PDBConstruct 2–99； UniProt 39–136 Author chain b； PDBConstruct 2–99； UniProt 39–136 Author chain g； PDBConstruct 2–99； UniProt 39–136 Author chain l； PDBConstruct 2–99； UniProt 39–136

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 CHLORIDE ION × 1 water × 10 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 3 water × 10 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Aprataxin and PNK-like factor × 2 （Q8IW19） GLYCEROL × 4 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1aoi 1kx3 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o

371 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name H4_XENLA
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 2–84； UniProt 21–103 Author chain I； PDBConstruct 2–84； UniProt 21–103 Author chain N； PDBConstruct 2–84； UniProt 21–103 Author chain S； PDBConstruct 2–84； UniProt 21–103 Author chain X； PDBConstruct 2–84； UniProt 21–103 Author chain c； PDBConstruct 2–84； UniProt 21–103 Author chain h； PDBConstruct 2–84； UniProt 21–103 Author chain m； PDBConstruct 2–84； UniProt 21–103

Aprataxin and PNK-like factor

Homo sapiens

UniProt Q8IW19

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） GLYCEROL × 3 CHLORIDE ION × 1 water × 10 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） GLYCEROL × 4 water × 9 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） GLYCEROL × 3 water × 10 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 10 Histone H2A × 2 （Q6AZJ8） Histone H2B × 2 （A0A1L8FQA5） Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） GLYCEROL × 4 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2kqb 2kqc 2kqd 2kqe 2kuo 5w7w 5w7w

7 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5e50 5e50 5w7x 5w7x 5w7x 5w7x 5w7y 5w7y 6erf 6erf 6erf 6erf

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name APLF_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 2–43； UniProt 449–490 Author chain J； PDBConstruct 2–43； UniProt 449–490 Author chain O； PDBConstruct 2–43； UniProt 449–490 Author chain T； PDBConstruct 2–43； UniProt 449–490 Author chain Y； PDBConstruct 2–43； UniProt 449–490 Author chain d； PDBConstruct 2–43； UniProt 449–490 Author chain i； PDBConstruct 2–43； UniProt 449–490 Author chain n； PDBConstruct 2–43； UniProt 449–490

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_id6yn1
Deposition date deposition_date2020-04-10
Structure title titleCrystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer
Keywords keywordsOctamer, aplf, chaperone, histone; CHAPERONE
Experimental Method methodX-RAY DIFFRACTION
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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.

6yn1__assembly_1__model_1

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

Download this curve (.dat)

6yn1__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.

6yn1__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）28.60 Å
Rg (electron density)27.41 Å
Total Rg28.35 Å
Atom count6189
Residues775
Excluded volume110600 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6yn1__assembly_1__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6yn1__assembly_2__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6yn1__assembly_3__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6yn1__assembly_4__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 (8)

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id6yn1B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1C01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1G01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1H01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1L01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1M01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1Q01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1R01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1V01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1W01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1X01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1a01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1b01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1c01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1f01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1g01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1k01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6yn1l01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
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7. Citations (1)