SAXSdb — 6qtv

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

E3 ubiquitin-protein ligase COP1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Transcription factor HFR1 × 1 （Q9FE22） MALONATE ION × 3 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COP1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–330； UniProt 349–675

Transcription factor HFR1

OrganismNot specified

UniProt Q9FE22

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase COP1 × 1 （P43254） MALONATE ION × 3 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HFR1_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–11； UniProt 57–66

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	6qtv
Deposition date deposition_date	2019-02-25
Structure title title	Crystal structure of an Arabidopsis WD40 domain in complex with an atypical bHLH transcription factor
Keywords keywords	Complex, PLANT PROTEIN; PLANT 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.

6qtv__assembly_1__model_1

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

Download this curve (.dat)

6qtv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qtv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.50 Å
Rg (electron density)	18.28 Å
Total Rg	19.28 Å
Atom count	4960
Residues	312
Excluded volume	44485 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qtv__assembly_1__model_1`	dimeric （2）	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	E3 ubiquitin-protein ligase COP1
Molecular weight formula_weight	37204.6 kDa
EC 编号 ec_number	2.3.2.27
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	5586

GAMTFTRYSRLRVIAEIRHGDIFHSANIVSSIEFDRDDELFATAGVSRCIKVFDFSSVVNEPADMQCPIVEMSTRSKLSCLSWNKHEKNHIASSDYEGIVTVWDVTTRQSLMEYEEHEKRAWSVDFSRTEPSMLVSGSDDCKVKVWCTRQEASVINIDMKANICCVKYNPGSSNYIAVGSADHHIHYYDLRNISQPLHVFSGHKKAVSYVKFLSNNELASASTDSTLRLWDVKDNLPVRTFRGHTNEKNFVGLTVNSEYLACGSETNEVYVYHKEITRPVTSHRFGSPDMDDAEEEAGSYFISAVCWKSDSPTMLTANSQGTIKVLVLAA

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Transcription factor HFR1
Molecular weight formula_weight	1267.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XYLQIVPEIHK

Entity 3 Entity 3 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	3

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	263

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6qtvA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	48.896 Å
Unit-cell length b length_b	55.089 Å
Unit-cell length c length_c	103.069 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	4

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

Resolution resolution	1.310 Å
Low-resolution limit resolution_low	48.580 Å
R factor r_factor	0.1353
R_work r_work	0.1332
R_free r_free	0.1761

Crystal structure of an Arabidopsis WD40 domain in complex with an atypical bHLH transcription factor

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

E3 ubiquitin-protein ligase COP1

State in the Current Structure

Other States of the Same Protein in the Database

Transcription factor HFR1

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

6qtv__assembly_1__model_1

6qtv__assembly_1__model_1 | I(q)

6qtv__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 non-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 an Arabidopsis WD40 domain in complex with an atypical bHLH transcription factor

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

E3 ubiquitin-protein ligase COP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcription factor HFR1

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

6qtv__assembly_1__model_1

6qtv__assembly_1__model_1 | I(q)

6qtv__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 non-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)