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 1.2 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: 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 remain ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 1A346Homo sapiensMutation(s): 0 
Gene Names: AOS1, SAE1, SUA1, UBLE1A
Find proteins for Q9UBE0 (Homo sapiens)
Explore Q9UBE0 
Go to UniProtKB:  Q9UBE0
NIH Common Fund Data Resources
PHAROS  Q9UBE0
GTEx  ENSG00000142230
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 2B660Homo sapiensMutation(s): 1 
Gene Names: HRIHFB2115, SAE2, UBA2, UBLE1B
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for Q9UBT2 (Homo sapiens)
Explore Q9UBT2 
Go to UniProtKB:  Q9UBT2
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PHAROS  Q9UBT2
GTEx  ENSG00000126261
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1D97Homo sapiensMutation(s): 1 
Gene Names: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165
GTEx  ENSG00000116030
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZU
Query on JZU
Download Ideal Coordinates CCD File 
D
5'-deoxy-5'-(sulfamoylamino)adenosine
C10 H15 N7 O5 S
RCHUICYCIUKUIY-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-12-05 
  • Released Date: 2010-02-16 
    • Deposition Author(s): Lima, C.D.

Revision History 

  • 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