3KYC

Human SUMO E1 complex with a SUMO1-AMP mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Active site remodelling accompanies thioester bond formation in the SUMO E1.

Olsen, S.K.Capili, A.D.Lu, X.Tan, D.S.Lima, C.D.

(2010) Nature 463: 906-912

  • DOI: https://doi.org/10.1038/nature08765
  • Primary Citation of Related Structures:  
    3KYC, 3KYD

  • PubMed Abstract: 

    E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 A, respectively. These structures show that side chain contacts to ATP.Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.


  • Organizational Affiliation

    Structural Biology, Sloan-Kettering Institute, New York, New York 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 1346Homo sapiensMutation(s): 0 
Gene Names: AOS1SAE1SUA1UBLE1A
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
SUMO-activating enzyme subunit 2660Homo sapiensMutation(s): 1 
Gene Names: HRIHFB2115SAE2UBA2UBLE1B
EC: 6.3.2
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
Small ubiquitin-related modifier 1C [auth D]97Homo sapiensMutation(s): 1 
Gene Names: OK/SW-cl.43SMT3CSMT3H3SUMO1UBL1
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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JZU
Query on JZU

Download Ideal Coordinates CCD File 
E [auth D]5'-deoxy-5'-(sulfamoylamino)adenosine
C10 H15 N7 O5 S
RCHUICYCIUKUIY-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.174α = 90
b = 133.365β = 90
c = 159.656γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2010-02-16 
  • Deposition Author(s): Lima, C.D.

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary