← Back to search
3dbh

Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg)

Method: X-RAY DIFFRACTION
▼

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

NEDD8-activating enzyme E1 regulatory subunit

Homo sapiens

UniProt Q13564

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） NEDD8 × 1 （Q15843） ZINC ION × 1 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
1r4m 1r4m 1r4m 1r4m 1r4n 1r4n 1r4n 1r4n 1yov 1yov 2nvu 3dbh

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ULA1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–531； UniProt 1–534 Author chain C； PDBConstruct 3–531； UniProt 1–534 Author chain E； PDBConstruct 3–531； UniProt 1–534 Author chain G； PDBConstruct 3–531； UniProt 1–534

NEDD8-activating enzyme E1 catalytic subunit

Homo sapiens

UniProt Q8TBC4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2lq7

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1r4m 1r4m 1r4m 1r4m 1r4n 1r4n 1r4n 1r4n 1y8x 1yov 1yov 2nvu

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBA3_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–434； UniProt 33–463 Author chain D； PDBConstruct 4–434； UniProt 33–463 Author chain F； PDBConstruct 4–434； UniProt 33–463 Author chain H； PDBConstruct 4–434； UniProt 33–463

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 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） ZINC ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） ZINC ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 NEDD8-activating enzyme E1 regulatory subunit × 1 （Q13564） NEDD8-activating enzyme E1 catalytic subunit × 1 （Q8TBC4） ZINC ION × 1 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 3
Chains and sequence ranges Author chain I； PDBConstruct 13–88； UniProt 1–76 Author chain J； PDBConstruct 13–88； UniProt 1–76 Author chain K； PDBConstruct 13–88； UniProt 1–76 Author chain L； PDBConstruct 13–88； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3dbh
Deposition date deposition_date2008-05-31
Structure title titleStructural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg)
Keywords keywords;Cell cycle, activating enzyme, Apoptosis, Membrane, Ubl conjugation pathway, ATP-binding, Ligase, Nucleotide-binding, Polymorphism, Nucleus ;; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

3dbh__assembly_1__model_1

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

Download this curve (.dat)

3dbh__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3dbh__assembly_1__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）31.68 Å
Rg (electron density)30.51 Å
Total Rg31.22 Å
Atom count8134
Residues1028
Excluded volume145170 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3dbh__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3dbh__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3dbh__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3dbh__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

▼

6. Fold Classification (SCOP + CATH) 37 domains

SCOP 2.08 (17 domains)

Domain ID domain_idd3dbha_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3dbhc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3dbhe_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3dbhg_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhh1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd3dbhh2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3dbhi2
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_idd3dbhi3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3dbhj_
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_idd3dbhk_
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_idd3dbhl_
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

CATH v4.4 (20 domains)

Domain ID domain_id3dbhA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id3dbhB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id3dbhC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id3dbhD03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id3dbhE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id3dbhF03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id3dbhG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3dbhH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id3dbhH03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id3dbhI00
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_id3dbhJ00
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_id3dbhK00
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_id3dbhL00
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
▶

7. Citations (1)