6ycq

Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA

Method: X-RAY DIFFRACTION

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

Auxin response factor 1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	21-7A × 1 21-7B × 1 CHLORIDE ION × 12 FORMIC ACID × 5 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 SODIUM ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARFA_ARATH
Isoform	Q8L7G0-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 1–355 Author chain B； PDBConstruct 1–355； UniProt 1–355

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	6ycq
Deposition date deposition_date	2020-03-18
Structure title title	Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA
Keywords keywords	Transcription Factor, DNA binding, Nucleus, Hormone Response, 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.

6ycq__assembly_1__model_1

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

Download this curve (.dat)

6ycq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ycq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.49 Å
Rg (electron density)	31.27 Å
Total Rg	32.02 Å
Atom count	6433
Residues	732
Excluded volume	110980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ycq__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 (8)

Entity 1 Entity 1 polymer

Description description	Auxin response factor 1
Molecular weight formula_weight	41079.4 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	7154

MAASNHSSGKPGGVLSDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQLEASMHQGLEQQMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPELDQSEPTSPDAPVQEPEKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFLRGENEELRVGVRRHMRQQTNIPSSVISSHSMHIGVLATAAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGEEAPEKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWELEPLNSYSQSM

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	21-7A
Molecular weight formula_weight	6430.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

TTGTCGGCCTTTGGCCGACAA

Entity 3 Entity 3 polymer

Description description	21-7B
Molecular weight formula_weight	6457.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTGTCGGCCAAAGGCCGACAA

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	648

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Unit-cell length a length_a	43.304 Å
Unit-cell length b length_b	102.784 Å
Unit-cell length c length_c	127.039 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.04 °
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	monoclinic

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	47.570 Å
R factor r_factor	0.1730
R_work r_work	0.1717
R_free r_free	0.1991

Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA

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

Auxin response factor 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

6ycq__assembly_1__model_1

6ycq__assembly_1__model_1 | I(q)

6ycq__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA

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

Auxin response factor 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

6ycq__assembly_1__model_1

6ycq__assembly_1__model_1 | I(q)

6ycq__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)