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Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg)

X-ray diffraction
3.05Å resolution
PDB entry 3dbr coloured by chain, front view.
PDB entry 3dbr coloured by chain, side view.
PDB entry 3dbr coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 and NEDD8
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Multimeric state: hetero trimer
Accessible surface area: 42039.81 Å2
Buried surface area: 10381.47 Å2
Dissociation area: 1,677.78 Å2
Dissociation energy (ΔGdiss): 9.82 kcal/mol
Dissociation entropy (TΔSdiss): 11.82 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-171762
Assembly 2
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Assembly Name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 and NEDD8
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Multimeric state: hetero trimer
Accessible surface area: 41163.92 Å2
Buried surface area: 10424.92 Å2
Dissociation area: 1,737.2 Å2
Dissociation energy (ΔGdiss): 8.61 kcal/mol
Dissociation entropy (TΔSdiss): 11.84 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-171762
Assembly 3
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Assembly Name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 and NEDD8
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Multimeric state: hetero trimer
Accessible surface area: 41376.39 Å2
Buried surface area: 10590.37 Å2
Dissociation area: 1,795.2 Å2
Dissociation energy (ΔGdiss): 8.3 kcal/mol
Dissociation entropy (TΔSdiss): 11.84 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-171762
Assembly 4
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Assembly Name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 and NEDD8
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Multimeric state: hetero trimer
Accessible surface area: 42292.08 Å2
Buried surface area: 10365.46 Å2
Dissociation area: 1,671.81 Å2
Dissociation energy (ΔGdiss): 7.46 kcal/mol
Dissociation entropy (TΔSdiss): 12.09 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-171762

Macromolecules

NEDD8-activating enzyme E1 regulatory subunit
Chains: A, C, E, G
Length: 531 amino acids
Theoretical weight: 59.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13564 (Residues: 1-534; Coverage: 99%)
Gene names: APPBP1, HPP1, NAE1
Pfam: ThiF family
InterPro:
CATH: NAD(P)-binding Rossmann-like Domain
SCOP: Ubiquitin activating enzymes (UBA)
NEDD8-activating enzyme E1 regulatory subunit in PDB entry 3dbr, assembly 1, front view.
NEDD8-activating enzyme E1 regulatory subunit in PDB entry 3dbr, assembly 1, side view.
NEDD8-activating enzyme E1 regulatory subunit in PDB entry 3dbr, assembly 1, top view.
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NEDD8-activating enzyme E1 catalytic subunit
Chains: B, D, F, H
Length: 434 amino acids
Theoretical weight: 48.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TBC4 (Residues: 33-463; Coverage: 93%)
Gene names: UBA3, UBE1C
Pfam:
InterPro:
CATH:
NEDD8-activating enzyme E1 catalytic subunit in PDB entry 3dbr, assembly 1, front view.
NEDD8-activating enzyme E1 catalytic subunit in PDB entry 3dbr, assembly 1, side view.
NEDD8-activating enzyme E1 catalytic subunit in PDB entry 3dbr, assembly 1, top view.
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NEDD8
Chains: I, J, K, L
Length: 88 amino acids
Theoretical weight: 9.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Pfam: Ubiquitin family
InterPro:
CATH: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
NEDD8 in PDB entry 3dbr, assembly 1, front view.
NEDD8 in PDB entry 3dbr, assembly 1, side view.
NEDD8 in PDB entry 3dbr, assembly 1, top view.
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