SAXSdb — 9inc

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H2A.Z

Homo sapiens

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 × 3	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 × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Histone H2B type 1-J × 2 （P06899） Vacuolar protein sorting-associated protein 72 homolog × 2 （Q15906） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2AZ_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–98； UniProt 17–114 Author chain D； PDBConstruct 1–98； UniProt 17–114

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 × 3	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 × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Histone H2A.Z × 2 （P0C0S5） Vacuolar protein sorting-associated protein 72 homolog × 2 （Q15906） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1J_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–92； UniProt 34–125 Author chain E； PDBConstruct 1–92； UniProt 34–125

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 × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Histone H2A.Z × 1 （P0C0S5） Histone H2B type 1-J × 1 （P06899） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Histone H2A.Z × 2 （P0C0S5） Histone H2B type 1-J × 2 （P06899） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS72_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 22–87； UniProt 8–73 Author chain F； PDBConstruct 22–87； UniProt 8–73

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_id	9inc
Deposition date deposition_date	2024-07-06
Last revision last_revision	2025-07-09
Structure title title	High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain
Keywords keywords	Histones and its chaperone, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method method	X-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.

9inc__assembly_1__model_1

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

Download this curve (.dat)

9inc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9inc__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.80 Å
Rg (electron density)	19.63 Å
Total Rg	20.47 Å
Atom count	1803
Residues	238
Excluded volume	31607 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9inc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9inc__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9inc__assembly_3__model_1`	hexameric （6）	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)

Entity 1 Entity 1 polymer

Description description	Histone H2A.Z
Molecular weight formula_weight	10521.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	3735

AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H2B type 1-J
Molecular weight formula_weight	10421.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSASS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Vacuolar protein sorting-associated protein 72 homolog
Molecular weight formula_weight	9567.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MGSSHHHHHHSSGLVPRGSHMAPRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSDFDIDEGDEPSSDG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

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Unit-cell length a length_a	116.093 Å
Unit-cell length b length_b	126.990 Å
Unit-cell length c length_c	70.757 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	39.770 Å
R factor r_factor	0.2214
R_work r_work	0.2195
R_free r_free	0.2573

High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H2A.Z

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B type 1-J

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein 72 homolog

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9inc__assembly_1__model_1

9inc__assembly_1__model_1 | I(q)

9inc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

7. Citations (1)

High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H2A.Z

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B type 1-J

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar protein sorting-associated protein 72 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9inc__assembly_1__model_1

9inc__assembly_1__model_1 | I(q)

9inc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

7. Citations (1)