SAXSdb — 6lqf

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

AT-rich interactive domain-containing protein 4

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	15-mer peptide from Histone H3.2 × 1 （P59226） ;DNA (5'-D(TPTPTPAPGPAPTPCPTPAPAPA)-3') ; × 2 ZINC ION × 3 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARID4_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–204； UniProt 545–747

15-mer peptide from Histone H3.2

OrganismNot specified

UniProt P59226

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	AT-rich interactive domain-containing protein 4 × 1 （Q6NQ79） ;DNA (5'-D(TPTPTPAPGPAPTPCPTPAPAPA)-3') ; × 2 ZINC ION × 3 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–15； UniProt 2–16

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	6lqf
Deposition date deposition_date	2020-01-13
Structure title title	Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide and DNA
Keywords keywords	ARID5, PHD finger, ARID domain, GENE REGULATION; GENE REGULATION
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.

6lqf__assembly_1__model_1

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

Download this curve (.dat)

6lqf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6lqf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.00 Å
Rg (electron density)	18.99 Å
Total Rg	19.93 Å
Atom count	1925
Residues	204
Excluded volume	32489 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6lqf__assembly_1__model_1`	tetrameric （4）	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	AT-rich interactive domain-containing protein 4
Molecular weight formula_weight	22936.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2133

SQIISLNPLPLKKHDCGRAHIQVCSEEEFLRDVMQFLLIRGHTRLVPPGGLAEFPDAVLNSKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYEYAHDDVDGECCLICRSSTAGDWVNCGSCGEWAHFGCDRRPGLGAFKDYAKTDGLEYVCPNCSVSNYRKKSQKTSNGGLLVP

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	15-mer peptide from Histone H3.2
Molecular weight formula_weight	1607.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ARTKQTARKSTGGKA

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(TPTPTPAPGPAPTPCPTPAPAPA)-3') ;
Molecular weight formula_weight	3660.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C

TTTAGATCTAAA

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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	208

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6lqfA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	60 — ARID DNA-binding domain

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Unit-cell length a length_a	56.173 Å
Unit-cell length b length_b	59.428 Å
Unit-cell length c length_c	92.958 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	25.035 Å
R factor r_factor	0.1759
R_work r_work	0.1750
R_free r_free	0.1916

Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide and DNA

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

AT-rich interactive domain-containing protein 4

State in the Current Structure

Other States of the Same Protein in the Database

15-mer peptide from Histone H3.2

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

6lqf__assembly_1__model_1

6lqf__assembly_1__model_1 | I(q)

6lqf__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide and DNA

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

AT-rich interactive domain-containing protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

15-mer peptide from Histone H3.2

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

6lqf__assembly_1__model_1

6lqf__assembly_1__model_1 | I(q)

6lqf__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)