6m2m

A role for histone chaperone OsChz1 in histone recognition and deposition

Method: X-RAY DIFFRACTION

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

Probable histone H2A.3

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Histone H2B.1 × 6 （Q9LQQ4） Expressed protein × 3 （Q2R2Z3） GLYCEROL × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A3_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–93； UniProt 14–106 Author chain C； PDBConstruct 1–93； UniProt 14–106 Author chain E； PDBConstruct 1–93； UniProt 14–106 Author chain G； PDBConstruct 1–93； UniProt 14–106 Author chain I； PDBConstruct 1–93； UniProt 14–106 Author chain K； PDBConstruct 1–93； UniProt 14–106

Histone H2B.1

Arabidopsis thaliana

UniProt Q9LQQ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Probable histone H2A.3 × 6 （O81826） Expressed protein × 3 （Q2R2Z3） GLYCEROL × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–98； UniProt 51–148 Author chain D； PDBConstruct 1–98； UniProt 51–148 Author chain F； PDBConstruct 1–98； UniProt 51–148 Author chain H； PDBConstruct 1–98； UniProt 51–148 Author chain J； PDBConstruct 1–98； UniProt 51–148 Author chain L； PDBConstruct 1–98； UniProt 51–148

Expressed protein

Oryza sativa subsp. japonica

UniProt Q2R2Z3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Probable histone H2A.3 × 6 （O81826） Histone H2B.1 × 6 （Q9LQQ4） GLYCEROL × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2R2Z3_ORYSJ
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–105； UniProt 367–471 Author chain N； PDBConstruct 1–105； UniProt 367–471 Author chain O； PDBConstruct 1–105； UniProt 367–471

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	6m2m
Deposition date deposition_date	2020-02-28
Structure title title	A role for histone chaperone OsChz1 in histone recognition and deposition
Keywords keywords	complex, CHAPERONE; CHAPERONE
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.

6m2m__assembly_1__model_1

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

Download this curve (.dat)

6m2m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6m2m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.40 Å
Rg (electron density)	32.18 Å
Total Rg	32.97 Å
Atom count	8006
Residues	1068
Excluded volume	143400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6m2m__assembly_1__model_1`	pentadecameric （15）	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 (5)

Entity 1 Entity 1 polymer

Description description	Probable histone H2A.3
Molecular weight formula_weight	10049.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A,C,G,I,K
Atom count atom_count	8020

KKSTSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIAN

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H2B.1
Molecular weight formula_weight	11033.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

KKRSKKNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Expressed protein
Molecular weight formula_weight	11448.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O

ILEKEGLSTNPSEKEIKAVKKRKERAKELEGIDMSNIITSSRRRSTSNFIPLPTPKIVADSDEDDEEDAEDDNDEEVNVEGGDEGDNDVGKAGDGSADDAEHDSD

Source Source

Source organism organism	Oryza sativa subsp. japonica
Common name common_name	Rice
NCBI taxonomy ID ncbi_taxonomy_id	39947
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6m2ma_
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	d6m2mb_
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	d6m2mc_
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	d6m2md_
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	d6m2me_
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	d6m2mf_
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	d6m2mg_
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	d6m2mh_
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	d6m2mi_
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	d6m2mj_
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	d6m2mk_
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	d6m2ml_
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 (1 domains)

Domain ID domain_id	6m2mL01
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	167.361 Å
Unit-cell length b length_b	116.336 Å
Unit-cell length c length_c	101.904 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1964
R_work r_work	0.1936
R_free r_free	0.2531

A role for histone chaperone OsChz1 in histone recognition and deposition

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

Probable histone H2A.3

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B.1

State in the Current Structure

Other States of the Same Protein in the Database

Expressed protein

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

6m2m__assembly_1__model_1

6m2m__assembly_1__model_1 | I(q)

6m2m__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (12 domains)

CATH v4.4 (1 domains)

7. Citations (1)

A role for histone chaperone OsChz1 in histone recognition and deposition

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

Probable histone H2A.3

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.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Expressed protein

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

6m2m__assembly_1__model_1

6m2m__assembly_1__model_1 | I(q)

6m2m__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (12 domains)

CATH v4.4 (1 domains)

7. Citations (1)