1Y8R

SUMO E1 ACTIVATING ENZYME SAE1-SAE2-SUMO1-MG-ATP COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1

Lois, L.M.Lima, C.D.

(2005) EMBO J 24: 439-451

  • DOI: https://doi.org/10.1038/sj.emboj.7600552
  • Primary Citation of Related Structures:  
    1Y8Q, 1Y8R

  • PubMed Abstract: 

    E1 enzymes facilitate conjugation of ubiquitin and ubiquitin-like proteins through adenylation, thioester transfer within E1, and thioester transfer from E1 to E2 conjugating proteins. Structures of human heterodimeric Sae1/Sae2-Mg.ATP and Sae1/Sae2-SUMO-1-Mg.ATP complexes were determined at 2.2 and 2.75 A resolution, respectively. Despite the presence of Mg.ATP, the Sae1/Sae2-SUMO-1-Mg.ATP structure reveals a substrate complex insomuch as the SUMO C-terminus remains unmodified within the adenylation site and 35 A from the catalytic cysteine, suggesting that additional changes within the adenylation site may be required to facilitate chemistry prior to adenylation and thioester transfer. A mechanism for E2 recruitment to E1 is suggested by biochemical and genetic data, each of which supports a direct role for the E1 C-terminal ubiquitin-like domain for E2 recruitment during conjugation.


  • Organizational Affiliation

    Structural Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like 1 activating enzyme E1A
A, D
346Homo sapiensMutation(s): 0 
Gene Names: UBLE1ASAE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBE0 (Homo sapiens)
Explore Q9UBE0 
Go to UniProtKB:  Q9UBE0
PHAROS:  Q9UBE0
GTEx:  ENSG00000142230 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBE0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like 2 activating enzyme E1B
B, E
640Homo sapiensMutation(s): 1 
Gene Names: UBLE1BSAE2
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT2 (Homo sapiens)
Explore Q9UBT2 
Go to UniProtKB:  Q9UBT2
PHAROS:  Q9UBT2
GTEx:  ENSG00000126261 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBT2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3C
C, F
97Homo sapiensMutation(s): 0 
Gene Names: UBL1SUMO-1SMT3CSMT3H3
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
GTEx:  ENSG00000116030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63165
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.197α = 90
b = 215.151β = 90
c = 100.87γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection