SAXSdb — 9ubd

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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 10	Histone H2B type 1-J × 4 （P06899） Helicase SRCAP × 2 （Q6ZRS2） water × 10	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 10	Histone H2A.Z × 4 （P0C0S5） Helicase SRCAP × 2 （Q6ZRS2） water × 10	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

Helicase SRCAP

OrganismNot specified

UniProt Q6ZRS2

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.Z × 4 （P0C0S5） Histone H2B type 1-J × 4 （P06899） water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRCAP_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–30； UniProt 531–560

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	9ubd
Deposition date deposition_date	2025-04-02
Last revision last_revision	2026-04-08
Structure title title	The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP Catalytic Subunit
Keywords keywords	Histone, Histone Variant, histone fold domain, DNA BINDING PROTEIN; DNA BINDING 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.

9ubd__assembly_1__model_1

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

Download this curve (.dat)

9ubd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ubd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.10 Å
Rg (electron density)	26.77 Å
Total Rg	27.61 Å
Atom count	5300
Residues	730
Excluded volume	93818 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ubd__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 (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	2685

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	E,B

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	Helicase SRCAP
Molecular weight formula_weight	3450.3 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SEDAQSQSQADEEEEDDDFGVEYLLARDEE

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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Unit-cell length a length_a	77.330 Å
Unit-cell length b length_b	102.190 Å
Unit-cell length c length_c	67.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.530 Å
Low-resolution limit resolution_low	35.100 Å
R factor r_factor	0.2537
R_work r_work	0.2523
R_free r_free	0.2884

The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP Catalytic Subunit

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

Helicase SRCAP

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

9ubd__assembly_1__model_1

9ubd__assembly_1__model_1 | I(q)

9ubd__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

Entity 4 Entity 4 water

7. Citations (1)

The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP Catalytic Subunit

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

Helicase SRCAP

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

9ubd__assembly_1__model_1

9ubd__assembly_1__model_1 | I(q)

9ubd__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

Entity 4 Entity 4 water

7. Citations (1)