2N1A

Docked structure between SUMO1 and ZZ-domain from CBP


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Analysis of a Complex between Small Ubiquitin-like Modifier 1 (SUMO1) and the ZZ Domain of CREB-binding Protein (CBP/p300) Reveals a New Interaction Surface on SUMO.

Diehl, C.Akke, M.Bekker-Jensen, S.Mailand, N.Streicher, W.Wikstrom, M.

(2016) J Biol Chem 291: 12658-12672

  • DOI: 10.1074/jbc.M115.711325
  • Primary Citation of Related Structures:  
    2N1A

  • PubMed Abstract: 
  • We have recently discovered that the ZZ zinc finger domain represents a novel small ubiquitin-like modifier (SUMO) binding motif. In this study we identify the binding epitopes in the ZZ domain of CBP (CREB-binding protein) and SUMO1 using NMR spectroscopy ...

    We have recently discovered that the ZZ zinc finger domain represents a novel small ubiquitin-like modifier (SUMO) binding motif. In this study we identify the binding epitopes in the ZZ domain of CBP (CREB-binding protein) and SUMO1 using NMR spectroscopy. The binding site on SUMO1 represents a unique epitope for SUMO interaction spatially opposite to that observed for canonical SUMO interaction motifs (SIMs). HADDOCK docking simulations using chemical shift perturbations and residual dipolar couplings was employed to obtain a structural model for the ZZ domain-SUMO1 complex. Isothermal titration calorimetry experiments support this model by showing that the mutation of key residues in the binding site abolishes binding and that SUMO1 can simultaneously and non-cooperatively bind both the ZZ domain and a canonical SIM motif. The binding dynamics of SUMO1 was further characterized using (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersions, which define the off rates for the ZZ domain and SIM motif and show that the dynamic binding process has different characteristics for the two cases. Furthermore, in the absence of bound ligands SUMO1 transiently samples a high energy conformation, which might be involved in ligand binding.


    Organizational Affiliation

    From the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark, Amgen Inc., Thousand Oaks, California 91320 mats.wikstrom@amgen.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1A103Homo sapiensMutation(s): 0 
Gene Names: OK/SW-cl.43SMT3CSMT3H3SUMO1UBL1
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS:  P63165
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CREB-binding proteinB53Homo sapiensMutation(s): 0 
Gene Names: CBPCREBBP
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
NIH Common Fund Data Resources
PHAROS:  Q92793
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2N1A Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-03-26 
  • Released Date: 2016-05-04 
  • Deposition Author(s): Diehl, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection