SAXSdb — 5igq

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

E3 ubiquitin-protein ligase RFWD2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tribbles homolog 1 × 1 （Q96RU8）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tribbles homolog 1 × 1 （Q96RU8）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Tribbles homolog 1 × 1 （Q96RU8）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Tribbles homolog 1 × 1 （Q96RU8）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Tribbles homolog 1 × 1 （Q96RU8）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Tribbles homolog 1 × 1 （Q96RU8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFWD2_HUMAN
Isoform	Q8NHY2-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–353； UniProt 161–506 Author chain B； PDBConstruct 8–353； UniProt 161–506 Author chain C； PDBConstruct 8–353； UniProt 161–506 Author chain D； PDBConstruct 8–353； UniProt 161–506 Author chain E； PDBConstruct 8–353； UniProt 161–506 Author chain F； PDBConstruct 8–353； UniProt 161–506

Tribbles homolog 1

OrganismNot specified

UniProt Q96RU8

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 RFWD2 × 1 （Q8NHY2）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RFWD2 × 1 （Q8NHY2）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RFWD2 × 1 （Q8NHY2）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RFWD2 × 1 （Q8NHY2）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RFWD2 × 1 （Q8NHY2）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RFWD2 × 1 （Q8NHY2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRIB1_HUMAN
Isoform	Q96RU8-2
PDB entities	2, 3
Chains and sequence ranges	Author chain U； PDBConstruct 1–11； UniProt 188–198 Author chain V； PDBConstruct 1–8； UniProt 188–195 Author chain W； PDBConstruct 1–8； UniProt 188–195 Author chain X； PDBConstruct 1–8； UniProt 188–195 Author chain Y； PDBConstruct 1–8； UniProt 188–195 Author chain Z； PDBConstruct 1–8； UniProt 188–195

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	5igq
Deposition date deposition_date	2016-02-28
Structure title title	WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) bound to peptide from Trib1
Keywords keywords	WD40 domain E3 ligase, Tribbles, Hydrolase-Peptide Complex; Hydrolase/Peptide
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.

5igq__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5igq__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5igq__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	19.67 Å
Rg (electron density)	18.60 Å
Total Rg	19.56 Å
Atom count	2551
Residues	332
Excluded volume	45213 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5igq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5igq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5igq__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5igq__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5igq__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5igq__assembly_6__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 (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase RFWD2
Molecular weight formula_weight	39932.9 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15349

MHHHHHHASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAANSQGTIKVLELV

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Tribbles homolog 1
Molecular weight formula_weight	1322.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

SDQIVPEYQED

Entity 3 Entity 3 polymer

Description description	Tribbles homolog 1
Molecular weight formula_weight	950.0 kDa
Source method src_method	syn
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V,W,X,Y,Z

SDQIVPEY

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5igqA00
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

Domain ID domain_id	5igqB00
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

Domain ID domain_id	5igqC00
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

Domain ID domain_id	5igqD00
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

Domain ID domain_id	5igqE00
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

Domain ID domain_id	5igqF00
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	247.646 Å
Unit-cell length b length_b	249.576 Å
Unit-cell length c length_c	124.512 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	48

Space group space_group	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	29.766 Å
R factor r_factor	0.2306
R_work r_work	0.2283
R_free r_free	0.2768

WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) bound to peptide from Trib1

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

E3 ubiquitin-protein ligase RFWD2

State in the Current Structure

Other States of the Same Protein in the Database

Tribbles homolog 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

5igq__assembly_4__model_1

5igq__assembly_4__model_1 | I(q)

5igq__assembly_4__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) bound to peptide from Trib1

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

E3 ubiquitin-protein ligase RFWD2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tribbles homolog 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

5igq__assembly_4__model_1

5igq__assembly_4__model_1 | I(q)

5igq__assembly_4__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)