SAXSdb — 7ybf

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

Histone H2B-alpha,Histone H2A-beta

Schizosaccharomyces pombe

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Spindle pole body-associated protein sad1 × 1 （Q09825） water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A2_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 96–189； UniProt 15–108 Author chain B； PDBConstruct 96–189； UniProt 15–108

Histone H2B-alpha,Histone H2A-beta

Schizosaccharomyces pombe

UniProt P04913

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Spindle pole body-associated protein sad1 × 1 （Q09825） water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 32–126 Author chain B； PDBConstruct 1–95； UniProt 32–126

Spindle pole body-associated protein sad1

Schizosaccharomyces pombe

UniProt Q09825

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Histone H2B-alpha,Histone H2A-beta × 1 （P04910,P04913） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAD1_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–17； UniProt 110–126

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_id	7ybf
Deposition date deposition_date	2022-06-29
Structure title title	Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B
Keywords keywords	Heterochromatin, Histone chaperone, Histone, Phase separation, MEMBRANE PROTEIN; MEMBRANE 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.

7ybf__assembly_1__model_1

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

Download this curve (.dat)

7ybf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ybf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.36 Å
Rg (electron density)	16.93 Å
Total Rg	18.02 Å
Atom count	1472
Residues	189
Excluded volume	26168 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ybf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7ybf__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Histone H2B-alpha,Histone H2A-beta
Molecular weight formula_weight	20717.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2951

NRKETYSSYIYKVLKQVHPDTGISNQAMRILNSFVNDIFERIATEASKLAAYNKKSTISSREIQTAVRLILPGELAKHAVTEGTKSVTKYSSSAQSAQSRSAKAGLAFPVGRVHRLLRKGNYAQRVGAGAPVYLAAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGHVTIAQGG

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Spindle pole body-associated protein sad1
Molecular weight formula_weight	2006.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ESDGDDEEFVNEEYENS

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	97

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Unit-cell length a length_a	42.804 Å
Unit-cell length b length_b	61.981 Å
Unit-cell length c length_c	76.016 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	37.190 Å
R factor r_factor	0.2028
R_work r_work	0.1980
R_free r_free	0.2481

Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B

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

Histone H2B-alpha,Histone H2A-beta

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B-alpha,Histone H2A-beta

State in the Current Structure

Other States of the Same Protein in the Database

Spindle pole body-associated protein sad1

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

7ybf__assembly_1__model_1

7ybf__assembly_1__model_1 | I(q)

7ybf__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B

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

Histone H2B-alpha,Histone H2A-beta

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-alpha,Histone H2A-beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Spindle pole body-associated protein sad1

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

7ybf__assembly_1__model_1

7ybf__assembly_1__model_1 | I(q)

7ybf__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)