4AUQ

Structure of BIRC7-UbcH5b-Ub complex.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.2 of the entry. See complete history. 


Literature

Birc7-E2 Ubiquitin Conjugate Structure Reveals the Mechanism of Ubiquitin Transfer by a Ring Dimer.

Dou, H., Buetow, L., Sibbet, G.J., Cameron, K., Huang, D.T.

(2012) Nat Struct Mol Biol 19: 876

  • DOI: 10.1038/nsmb.2379
  • Primary Citation of Related Structures:  
    4AUQ

  • PubMed Abstract: 

    • Certain RING ubiquitin ligases (E3s) dimerize to facilitate ubiquitin (Ub) transfer from ubiquitin-conjugating enzyme (E2) to substrate, but structural evidence on how this process promotes Ub transfer is lacking. Here we report the structure of the human dimeric RING domain from BIRC7 in complex with the E2 UbcH5B covalently linked to Ub (UbcH5B∼Ub) ...

    Certain RING ubiquitin ligases (E3s) dimerize to facilitate ubiquitin (Ub) transfer from ubiquitin-conjugating enzyme (E2) to substrate, but structural evidence on how this process promotes Ub transfer is lacking. Here we report the structure of the human dimeric RING domain from BIRC7 in complex with the E2 UbcH5B covalently linked to Ub (UbcH5B∼Ub). The structure reveals extensive noncovalent donor Ub interactions with UbcH5B and both subunits of the RING domain dimer that stabilize the globular body and C-terminal tail of Ub. Mutations that disrupt these noncovalent interactions or RING dimerization reduce UbcH5B∼Ub binding affinity and ubiquitination activity. Moreover, NMR analyses demonstrate that BIRC7 binding to UbcH5B∼Ub induces peak-shift perturbations in the donor Ub consistent with the crystallographically-observed Ub interactions. Our results provide structural insights into how dimeric RING E3s recruit E2∼Ub and optimize the donor Ub configuration for transfer.

    Organizational Affiliation: 

    The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 D2A, D147Homo sapiensMutation(s): 3 
Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
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Find proteins for P62837 (Homo sapiens)
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PHAROS:  P62837
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UniProt GroupP62837
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7B, E62Homo sapiensMutation(s): 0 
Gene Names: BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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Find proteins for Q96CA5 (Homo sapiens)
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PHAROS:  Q96CA5
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UniProt GroupQ96CA5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-CC, F81Homo sapiensMutation(s): 0 
Gene Names: UBC
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Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
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UniProt GroupP0CG48
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.64α = 90
b = 100.64β = 90
c = 123.899γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations