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5fug

Crystal structure of a human YL1-H2A.Z-H2B complex

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

HISTONE H2A.Z

HOMO SAPIENS

UniProt P0C0S5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 HISTONE H2B TYPE 1-J × 1 （P06899） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 HISTONE H2B TYPE 1-J × 1 （P06899） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 HISTONE H2B TYPE 1-J × 1 （P06899） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 HISTONE H2B TYPE 1-J × 1 （P06899） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 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
3wa9 4cay 4nft 4nft 4nft 4nft 5b31 5b32 5b33 5chl 5fug 5fug

34 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name H2AZ_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–110； UniProt 19–128 Author chain D； PDBConstruct 1–110； UniProt 19–128 Author chain G； PDBConstruct 1–110； UniProt 19–128 Author chain J； PDBConstruct 1–110； UniProt 19–128

HISTONE H2B TYPE 1-J

HOMO SAPIENS

UniProt P06899

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG × 1 （Q15906） water × 1 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
2rvq 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi

302 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name H2B1J_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–96； UniProt 31–126 Author chain E； PDBConstruct 1–96； UniProt 31–126 Author chain H； PDBConstruct 1–96； UniProt 31–126 Author chain K； PDBConstruct 1–96； UniProt 31–126

VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG

HOMO SAPIENS

UniProt Q15906

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） HISTONE H2B TYPE 1-J × 1 （P06899） water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） HISTONE H2B TYPE 1-J × 1 （P06899） water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） HISTONE H2B TYPE 1-J × 1 （P06899） water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 HISTONE H2A.Z × 1 （P0C0S5） HISTONE H2B TYPE 1-J × 1 （P06899） water × 1 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
5fug 5fug 5fug 5fug 8qr1 8x15 8x19 8x1c 8xvg 8xvt 9c57 9c62

22 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VPS72_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 5–68； UniProt 6–69 Author chain F； PDBConstruct 5–68； UniProt 6–69 Author chain I； PDBConstruct 5–68； UniProt 6–69 Author chain L； PDBConstruct 5–68； UniProt 6–69

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_id5fug
Deposition date deposition_date2016-01-27
Structure title titleCrystal structure of a human YL1-H2A.Z-H2B complex
Keywords keywordsDNA BINDING PROTEIN, HISTONE, CHAPERONE, REMODELER, H2A.Z, YL1; DNA BINDING PROTEIN
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.

5fug__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5fug__assembly_3__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5fug__assembly_3__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）19.89 Å
Rg (electron density)18.51 Å
Total Rg19.59 Å
Atom count1783
Residues230
Excluded volume31433 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5fug__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5fug__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5fug__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5fug__assembly_4__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5fuga_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones
Domain ID domain_idd5fugb_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones
Domain ID domain_idd5fugd_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones
Domain ID domain_idd5fuge_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones
Domain ID domain_idd5fugg_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones
Domain ID domain_idd5fugh_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones
Domain ID domain_idd5fugj_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones
Domain ID domain_idd5fugk_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.1 — Nucleosome core histones

CATH v4.4 (8 domains)

Domain ID domain_id5fugA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id5fugB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id5fugD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id5fugE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id5fugG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id5fugH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id5fugJ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id5fugK00
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)