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3o6b

A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) low resolution

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

Defective in cullin neddylation protein 1

Saccharomyces cerevisiae

UniProt Q12395

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Cell division control protein 53 × 1 （Q12018） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Cell division control protein 53 × 1 （Q12018） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Cell division control protein 53 × 1 （Q12018） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Cell division control protein 53 × 1 （Q12018） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Cell division control protein 53 × 1 （Q12018） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2is9 2l4e 2l4f 3o2p

4 assemblies

Homodimer
2is9 3bq3

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3o2p 3o6b 3o6b 3o6b 3o6b 3o6b 3tdi 3tdi 3tdi

9 assemblies

View Construct and Data Evidence
UniProt name DCN1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–202； UniProt 70–269 Author chain C； PDBConstruct 3–202； UniProt 70–269 Author chain E； PDBConstruct 3–202； UniProt 70–269 Author chain G； PDBConstruct 3–202； UniProt 70–269 Author chain I； PDBConstruct 3–202； UniProt 70–269

Cell division control protein 53

Saccharomyces cerevisiae

UniProt Q12018

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Defective in cullin neddylation protein 1 × 1 （Q12395） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Defective in cullin neddylation protein 1 × 1 （Q12395） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Defective in cullin neddylation protein 1 × 1 （Q12395） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Defective in cullin neddylation protein 1 × 1 （Q12395） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Defective in cullin neddylation protein 1 × 1 （Q12395） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3o2p

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3o2p 3o6b 3o6b 3o6b 3o6b 3o6b

6 assemblies

View Construct and Data Evidence
UniProt name CDC53_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–76； UniProt 742–815 Author chain D； PDBConstruct 3–76； UniProt 742–815 Author chain F； PDBConstruct 3–76； UniProt 742–815 Author chain H； PDBConstruct 3–76； UniProt 742–815 Author chain J； PDBConstruct 3–76； UniProt 742–815

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_id3o6b
Deposition date deposition_date2010-07-28
Structure title titleA Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) low resolution
Keywords keywordsLigase, Cell Cycle; Ligase, Cell Cycle
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.

3o6b__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3o6b__assembly_5__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3o6b__assembly_5__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）21.81 Å
Rg (electron density)20.78 Å
Total Rg21.91 Å
Atom count1822
Residues218
Excluded volume32772 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3o6b__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3o6b__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3o6b__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3o6b__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3o6b__assembly_5__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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id3o6bA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3o6bB00
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_id3o6bC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3o6bC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily200 — Cullin, PONY binding domain
Domain ID domain_id3o6bD00
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_id3o6bE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3o6bE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily200 — Cullin, PONY binding domain
Domain ID domain_id3o6bF00
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_id3o6bG01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3o6bH00
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_id3o6bI01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3o6bJ00
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
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7. Citations (1)