4p5o

Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action

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 5	E3 ubiquitin-protein ligase RBX1 × 1 （P62877） DCN1-like protein 1 × 1 （Q96GG9） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） NEDD8 × 1 （Q15843） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	E3 ubiquitin-protein ligase RBX1 × 1 （P62877） DCN1-like protein 1 × 1 （Q96GG9） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） NEDD8 × 1 （Q15843） 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

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 5	Cullin-1 × 1 （Q13616） DCN1-like protein 1 × 1 （Q96GG9） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） NEDD8 × 1 （Q15843） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Cullin-1 × 1 （Q13616） DCN1-like protein 1 × 1 （Q96GG9） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） NEDD8 × 1 （Q15843） 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 1–106； UniProt 3–108 Author chain D； PDBConstruct 1–106； UniProt 3–108

DCN1-like protein 1

Homo sapiens

UniProt Q96GG9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） NEDD8 × 1 （Q15843） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） NEDD8 × 1 （Q15843） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCNL1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 3–200； UniProt 62–259 Author chain F； PDBConstruct 3–200； UniProt 62–259

NEDD8-conjugating enzyme Ubc12

Homo sapiens

UniProt P61081

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） DCN1-like protein 1 × 1 （Q96GG9） NEDD8 × 1 （Q15843） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） DCN1-like protein 1 × 1 （Q96GG9） NEDD8 × 1 （Q15843） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC12_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 2–183； UniProt 2–183 Author chain I； PDBConstruct 2–183； UniProt 2–183

NEDD8

Homo sapiens

UniProt Q15843

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） DCN1-like protein 1 × 1 （Q96GG9） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） DCN1-like protein 1 × 1 （Q96GG9） NEDD8-conjugating enzyme Ubc12 × 1 （P61081） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEDD8_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain H； PDBConstruct 6–81； UniProt 1–76 Author chain K； PDBConstruct 6–81； UniProt 1–76

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	4p5o
Deposition date deposition_date	2014-03-18
Structure title title	Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action
Keywords keywords	Nedd8, Cullin, Neddylation, Complex, Ubc12, Dcn1, ubiquitin, 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.

4p5o__assembly_1__model_1

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

Download this curve (.dat)

4p5o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4p5o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.31 Å
Rg (electron density)	32.64 Å
Total Rg	33.20 Å
Atom count	6832
Residues	843
Excluded volume	122290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4p5o__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4p5o__assembly_2__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Cullin-1
Molecular weight formula_weight	42722.1 kDa
Mutation mutation	L421E, V451E, V452K, Y455K, K720R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	13577

GSMAQSSSKSPEELARYCDSLLKKSSKNPEEAELEDTLNQVMEKFKKIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMRMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

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	2

Polymer Polymer

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

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 polymer

Description description	DCN1-like protein 1
Molecular weight formula_weight	23237.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

GSRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV

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 4 Entity 4 polymer

Description description	NEDD8-conjugating enzyme Ubc12
Molecular weight formula_weight	21754.8 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	N103S, C111S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,G

MIKLFSLKQQKKEEESAGGTKGSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPSIDLEGNVSLNILREDWKPVLTINSIIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFERCLKHHHHHH

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 5 Entity 5 polymer

Description description	NEDD8
Molecular weight formula_weight	8919.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,H

GSGGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG

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 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d4p5oa1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.40 — Cullin homology domain
Superfamily Superfamily superfamily	e.40.1 — Cullin homology domain
Family Family family	e.40.1.1 — Cullin homology domain

Domain ID domain_id	d4p5oa2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.34 — SCF ubiquitin ligase complex WHB domain

Domain ID domain_id	d4p5ob_
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

Domain ID domain_id	d4p5oc1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.40 — Cullin homology domain
Superfamily Superfamily superfamily	e.40.1 — Cullin homology domain
Family Family family	e.40.1.1 — Cullin homology domain

Domain ID domain_id	d4p5oc2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.34 — SCF ubiquitin ligase complex WHB domain

Domain ID domain_id	d4p5od_
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

Domain ID domain_id	d4p5og1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d4p5og2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p5og3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p5oh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d4p5oi1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d4p5oi2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p5oi3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p5ok_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (12 domains)

Domain ID domain_id	4p5oA01
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	4p5oA02
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	4p5oA03
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	4p5oB00
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	4p5oC01
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	4p5oC02
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	4p5oC03
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	4p5oD00
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	4p5oE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4p5oF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4p5oG01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	4p5oI01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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Unit-cell length a length_a	89.105 Å
Unit-cell length b length_b	129.606 Å
Unit-cell length c length_c	119.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.79 °
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	—

Resolution resolution	3.107 Å
Low-resolution limit resolution_low	42.133 Å
R factor r_factor	0.2303
R_work r_work	0.2274
R_free r_free	0.2843

Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action

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

DCN1-like protein 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

NEDD8-conjugating enzyme Ubc12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NEDD8

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

4p5o__assembly_1__model_1

4p5o__assembly_1__model_1 | I(q)

4p5o__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)