SAXSdb — 6kbb

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

Histone H2A type 1-D

Homo sapiens

UniProt P20671

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 2-E × 1 （Q16778） SWR1-complex protein 5 × 1 （P38326） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Histone H2B type 2-E × 1 （Q16778） SWR1-complex protein 5 × 1 （P38326） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1D_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–96； UniProt 14–107 Author chain C； PDBConstruct 3–96； UniProt 14–107

Histone H2B type 2-E

Homo sapiens

UniProt Q16778

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 type 1-D × 1 （P20671） SWR1-complex protein 5 × 1 （P38326） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Histone H2A type 1-D × 1 （P20671） SWR1-complex protein 5 × 1 （P38326） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B2E_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–104； UniProt 27–126 Author chain D； PDBConstruct 5–104； UniProt 27–126

SWR1-complex protein 5

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38326

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 type 1-D × 1 （P20671） Histone H2B type 2-E × 1 （Q16778） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Histone H2A type 1-D × 1 （P20671） Histone H2B type 2-E × 1 （Q16778） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SWC5_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 3–81； UniProt 1–79 Author chain F； PDBConstruct 3–81； UniProt 1–79

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	6kbb
Deposition date deposition_date	2019-06-24
Structure title title	Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition
Keywords keywords	Histone chaperone, TRANSCRIPTION; TRANSCRIPTION
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.

6kbb__assembly_1__model_1

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

Download this curve (.dat)

6kbb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6kbb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.31 Å
Rg (electron density)	17.80 Å
Total Rg	18.78 Å
Atom count	1535
Residues	194
Excluded volume	27160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6kbb__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6kbb__assembly_2__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)

Entity 1 Entity 1 polymer

Description description	Histone H2A type 1-D
Molecular weight formula_weight	10466.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A
Atom count atom_count	3067

GSKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGG

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

Entity 2 Entity 2 polymer

Description description	Histone H2B type 2-E
Molecular weight formula_weight	11645.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGSMGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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

Entity 3 Entity 3 polymer

Description description	SWR1-complex protein 5
Molecular weight formula_weight	8942.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSMPEVETKIIPNEKEDEDEDGYIEEEDEDFQPEKDKLGGGSDDSDASDGGDDYDDGVNRDKGRNKVDYSRIESESGGLIK

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	59

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6kbba_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d6kbbb_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d6kbbc_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d6kbbd_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

CATH v4.4 (4 domains)

Domain ID domain_id	6kbbA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6kbbB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6kbbC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6kbbD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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Unit-cell length a length_a	107.072 Å
Unit-cell length b length_b	65.521 Å
Unit-cell length c length_c	84.821 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.83 °
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	2.365 Å
Low-resolution limit resolution_low	44.986 Å
R factor r_factor	0.1894
R_work r_work	0.1876
R_free r_free	0.2256

Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition

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

Histone H2A type 1-D

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B type 2-E

State in the Current Structure

Other States of the Same Protein in the Database

SWR1-complex protein 5

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

6kbb__assembly_1__model_1

6kbb__assembly_1__model_1 | I(q)

6kbb__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

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition

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

Histone H2A type 1-D

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 2-E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SWR1-complex protein 5

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

6kbb__assembly_1__model_1

6kbb__assembly_1__model_1 | I(q)

6kbb__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

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)