6NNQ

Non-covalent structure of SENP1 in complex with SUMO2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Noncovalent structure of SENP1 in complex with SUMO2.

Ambaye, N.D.

(2019) Acta Crystallogr F Struct Biol Commun 75: 332-339

  • DOI: 10.1107/S2053230X19004266
  • Primary Citation of Related Structures:  
    6NNQ

  • PubMed Abstract: 
  • SUMOylation is a post-translational modification in which a small ubiquitin-like molecule (SUMO) is appended to substrate proteins and is known to influence myriads of biological processes. A delicate interplay between several families of SUMOylation proteins and their substrates ensures the proper level of SUMOylation required for normal cell function ...

    SUMOylation is a post-translational modification in which a small ubiquitin-like molecule (SUMO) is appended to substrate proteins and is known to influence myriads of biological processes. A delicate interplay between several families of SUMOylation proteins and their substrates ensures the proper level of SUMOylation required for normal cell function. Among the SUMO proteins, SUMO2 is known to form mono-SUMOylated proteins and engage in poly-SUMO chain formation, while sentrin-specific protease 1 (SENP1) is a key enzyme in regulating both events. Determination of the SENP1-SUMO2 interaction is therefore necessary to better understand SUMOylation. In this regard, the current paper reports the noncovalent structure of SENP1 in complex with SUMO2, which was refined to a resolution of 2.62 Å with R and R free values of 22.92% and 27.66%, respectively. The structure shows that SENP1-SUMO2 complex formation is driven largely by polar interactions and limited hydrophobic contacts. The essential C-terminal motif (QQTGG) of SUMO2 is stabilized by a number of specific bonding interactions that enable it to protrude into the catalytic triad of SENP1 and provide the arrangement necessary for maturation of SUMO and deSUMOylation activity. Overall, the structure shows a number of structural details that pinpoint the basis of SENP1-SUMO2 complex formation.


    Organizational Affiliation

    Department of Immune-Oncology, Beckman Research Institute, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sentrin-specific protease 1A224Homo sapiensMutation(s): 0 
Gene Names: SENP1
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0U3 (Homo sapiens)
Explore Q9P0U3 
Go to UniProtKB:  Q9P0U3
PHAROS:  Q9P0U3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P0U3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 3B78Homo sapiensMutation(s): 0 
Gene Names: SUMO3SMT3ASMT3H1
UniProt & NIH Common Fund Data Resources
Find proteins for P55854 (Homo sapiens)
Explore P55854 
Go to UniProtKB:  P55854
PHAROS:  P55854
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55854
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.732α = 90
b = 98.732β = 90
c = 101.805γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2019-01-15 
  • Released Date: 2019-05-08 
  • Deposition Author(s): Ambaye, N.D.

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references