3rtr

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases

Method: X-RAY DIFFRACTION

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

Cullin-1

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	E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–368； UniProt 411–776 Author chain C； PDBConstruct 3–368； UniProt 411–776 Author chain E； PDBConstruct 3–368； UniProt 411–776 Author chain G； PDBConstruct 3–368； UniProt 411–776

E3 ubiquitin-protein ligase RBX1

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cullin-1 × 1 （Q13616） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cullin-1 × 1 （Q13616） ZINC ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Cullin-1 × 1 （Q13616） ZINC ION × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Cullin-1 × 1 （Q13616） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBX1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–106； UniProt 5–108 Author chain D； PDBConstruct 3–106； UniProt 5–108 Author chain F； PDBConstruct 3–106； UniProt 5–108 Author chain H； PDBConstruct 3–106； UniProt 5–108

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	3rtr
Deposition date deposition_date	2011-05-03
Structure title title	A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases
Keywords keywords	UBIQUITIN, NEDD8, CULLIN, UBL CONJUGATION PATHWAY, E3 LIGASE, LIGASE; LIGASE
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.

3rtr__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3rtr__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rtr__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	26.43 Å
Rg (electron density)	25.32 Å
Total Rg	26.27 Å
Atom count	3253
Residues	396
Excluded volume	58315 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rtr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rtr__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3rtr__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3rtr__assembly_4__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	Cullin-1
Molecular weight formula_weight	42694.0 kDa
Mutation mutation	L421E, V451E, V452K, Y455K
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	14055

GSMAQSSSKSPEELARYCDSLLKKSSKNPEEAELEDTLNQVMEKFKKIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase RBX1
Molecular weight formula_weight	12089.7 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3rtrA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	3rtrA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	130 — Cullin; Chain C, Domain 2

Domain ID domain_id	3rtrA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3rtrB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3rtrC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	3rtrC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	130 — Cullin; Chain C, Domain 2

Domain ID domain_id	3rtrC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3rtrD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3rtrE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	3rtrE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	130 — Cullin; Chain C, Domain 2

Domain ID domain_id	3rtrE03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3rtrF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3rtrG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	3rtrG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	130 — Cullin; Chain C, Domain 2

Domain ID domain_id	3rtrG03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3rtrH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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Unit-cell length a length_a	88.475 Å
Unit-cell length b length_b	119.796 Å
Unit-cell length c length_c	231.861 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	3.210 Å
Low-resolution limit resolution_low	29.949 Å
R factor r_factor	—
R_work r_work	0.2377
R_free r_free	0.2825

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases

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

Cullin-1

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin-protein ligase RBX1

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

3rtr__assembly_3__model_1

3rtr__assembly_3__model_1 | I(q)

3rtr__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases

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

Cullin-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

E3 ubiquitin-protein ligase RBX1

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

3rtr__assembly_3__model_1

3rtr__assembly_3__model_1 | I(q)

3rtr__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)