3TDU

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex.

Scott, D.C.Monda, J.K.Bennett, E.J.Harper, J.W.Schulman, B.A.

(2011) Science 334: 674-678

  • DOI: https://doi.org/10.1126/science.1209307
  • Primary Citation of Related Structures:  
    3TDI, 3TDU, 3TDZ

  • PubMed Abstract: 

    Although many eukaryotic proteins are amino (N)-terminally acetylated, structural mechanisms by which N-terminal acetylation mediates protein interactions are largely unknown. Here, we found that N-terminal acetylation of the E2 enzyme, Ubc12, dictates distinctive E3-dependent ligation of the ubiquitin-like protein Nedd8 to Cul1. Structural, biochemical, biophysical, and genetic analyses revealed how complete burial of Ubc12's N-acetyl-methionine in a hydrophobic pocket in the E3, Dcn1, promotes cullin neddylation. The results suggest that the N-terminal acetyl both directs Ubc12's interactions with Dcn1 and prevents repulsion of a charged N terminus. Our data provide a link between acetylation and ubiquitin-like protein conjugation and define a mechanism for N-terminal acetylation-dependent recognition.


  • Organizational Affiliation

    Structural Biology Department, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DCN1-like protein 1
A, B
200Homo sapiensMutation(s): 0 
Gene Names: DCUN1D1DCUN1L1RP42SCCRO
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GG9 (Homo sapiens)
Explore Q96GG9 
Go to UniProtKB:  Q96GG9
PHAROS:  Q96GG9
GTEx:  ENSG00000043093 
Entity Groups  
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UniProt GroupQ96GG9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-1
C, D
77Homo sapiensMutation(s): 0 
Gene Names: CUL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13616 (Homo sapiens)
Explore Q13616 
Go to UniProtKB:  Q13616
PHAROS:  Q13616
GTEx:  ENSG00000055130 
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UniProt GroupQ13616
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD8-conjugating enzyme Ubc12
E, F
16Homo sapiensMutation(s): 1 
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61081 (Homo sapiens)
Explore P61081 
Go to UniProtKB:  P61081
PHAROS:  P61081
GTEx:  ENSG00000130725 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61081
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.431α = 90
b = 65.454β = 104.73
c = 64.182γ = 90
Software Package:
Software NamePurpose
BSSdata collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-11-23
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.3: 2018-04-18
    Changes: Data collection
  • Version 1.4: 2020-01-29
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2023-09-13
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.6: 2024-03-13
    Changes: Derived calculations