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3dqv

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 3 Cullin-5 × 1 （Q93034） Rbx1 × 1 （P62877） ZINC ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Cullin-5 × 1 （Q93034） Rbx1 × 1 （P62877） ZINC ION × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 Cullin-5 × 2 （Q93034） Rbx1 × 2 （P62877） ZINC ION × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ndd 1ndd 1ndd 1ndd 2ko3

5 assemblies

Homodimer

None

Homotetramer
1ndd

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1r4m 1r4m 1r4m 1r4m 1r4n 1r4n 1r4n 1r4n 1xt9 2bkr 2n7k 2nvu

66 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NEDD8_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–81； UniProt 1–76 Author chain B； PDBConstruct 6–81； UniProt 1–76

Cullin-5

Homo sapiens

UniProt Q93034

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 NEDD8 × 1 （Q15843） Rbx1 × 1 （P62877） ZINC ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 NEDD8 × 1 （Q15843） Rbx1 × 1 （P62877） ZINC ION × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 NEDD8 × 2 （Q15843） Rbx1 × 2 （P62877） ZINC ION × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3dpl 3dqv 3dqv 3dqv 4jgh 4jgh 4n9f 4n9f 4n9f 4n9f 4n9f 4n9f

28 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CUL5_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 3–382； UniProt 401–780 Author chain D； PDBConstruct 3–382； UniProt 401–780

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 3 NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） ZINC ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 NEDD8 × 1 （Q15843） Cullin-5 × 1 （Q93034） ZINC ION × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 6 NEDD8 × 2 （Q15843） Cullin-5 × 2 （Q93034） ZINC ION × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2lgv

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ldj 1ldk 1ldk 1u6g 29hg 29hh 29hi 2hye 3dpl 3dqv 3dqv 3dqv

107 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RBX1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain R； PDBConstruct 3–106； UniProt 5–108 Author chain Y； 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_id3dqv
Deposition date deposition_date2008-07-09
Structure title titleStructural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation
Keywords keywords;ubiquitin, nedd8, scf, cullin-ring ligase, cullin, Nucleus, Ubl conjugation pathway, Host-virus interaction, Receptor, Ubl conjugation, Acetylation, Cytoplasm, DNA damage, DNA repair, Metal-binding, Zinc, Zinc-finger, SIGNALING PROTEIN, LIGASE ;; LIGASE
Experimental Method methodX-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.

3dqv__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dqv__assembly_2__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3dqv__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）31.18 Å
Rg (electron density)30.34 Å
Total Rg30.96 Å
Atom count4404
Residues523
Excluded volume79405 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3dqv__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3dqv__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3dqv__assembly_3__model_1 hexameric （6） 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 (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3dqva2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3dqva3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3dqvb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3dqvb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3dqvr_
Class classg — Small proteins
Fold Fold foldg.44 — RING/U-box
Superfamily Superfamily superfamilyg.44.1 — RING/U-box
Family Family familyg.44.1.1 — RING finger domain, C3HC4
Domain ID domain_idd3dqvy_
Class classg — Small proteins
Fold Fold foldg.44 — RING/U-box
Superfamily Superfamily superfamilyg.44.1 — RING/U-box
Family Family familyg.44.1.1 — RING finger domain, C3HC4

CATH v4.4 (10 domains)

Domain ID domain_id3dqvA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3dqvB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3dqvC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily10 — Cullin Repeats
Domain ID domain_id3dqvC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily130 — Cullin; Chain C, Domain 2
Domain ID domain_id3dqvC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id3dqvD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily10 — Cullin Repeats
Domain ID domain_id3dqvD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily130 — Cullin; Chain C, Domain 2
Domain ID domain_id3dqvD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id3dqvR00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id3dqvY00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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7. Citations (1)