SAXSdb — 1yd9

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

Core histone macro-H2A.1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GOLD ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GOLD ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GOLD ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GOLD ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2AY_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 51–193； UniProt 228–370 Author chain B； PDBConstruct 51–193； UniProt 228–370 Author chain C； PDBConstruct 51–193； UniProt 228–370 Author chain D； PDBConstruct 51–193； UniProt 228–370

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	1yd9
Deposition date deposition_date	2004-12-23
Structure title title	1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MacroH2A1.1.
Keywords keywords	Alpha-Beta Structure, A1pp Domain, Macro-Domain, STRUCTURAL PROTEIN; STRUCTURAL 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.

1yd9__assembly_1__model_1

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

Download this curve (.dat)

1yd9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yd9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.80 Å
Rg (electron density)	15.43 Å
Total Rg	16.69 Å
Atom count	1415
Residues	188
Excluded volume	25511 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yd9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yd9__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yd9__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yd9__assembly_4__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	Core histone macro-H2A.1
Molecular weight formula_weight	20538.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6173

GPLGSGFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGSTLEKKGGKEFVEAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVWGSDKCEELLEKTVKNCLALADDRKLKSIAFPSIGSGRNGFPKQTAAQLILKAISSYFVSTMSSSIKTVYFVLFDSESIGIYVQEMAKLDAN

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GOLD ION
Molecular weight formula_weight	197.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	540

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1yd9a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.2 — Macro domain

Domain ID domain_id	d1yd9b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.0 — automated matches

Domain ID domain_id	d1yd9c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.0 — automated matches

Domain ID domain_id	d1yd9c3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1yd9d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	1yd9A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1yd9B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1yd9C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1yd9D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

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Unit-cell length a length_a	83.114 Å
Unit-cell length b length_b	89.791 Å
Unit-cell length c length_c	95.679 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2350
R_free r_free	0.2600

1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MacroH2A1.1.

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

Core histone macro-H2A.1

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

1yd9__assembly_1__model_1

1yd9__assembly_1__model_1 | I(q)

1yd9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MacroH2A1.1.

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

Core histone macro-H2A.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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yd9__assembly_1__model_1

1yd9__assembly_1__model_1 | I(q)

1yd9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)