3RZW

Crystal Structure of the Monobody ySMB-9 bound to human SUMO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.

Koide, A.Wojcik, J.Gilbreth, R.N.Hoey, R.J.Koide, S.

(2012) J.Mol.Biol. 415: 393-405

  • DOI: 10.1016/j.jmb.2011.12.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The fibronectin type III domain (FN3) has become one of the most widely used non-antibody scaffolds for generating new binding proteins. Because of its structural homology to the immunoglobulin domain, combinatorial libraries of FN3 designed to date ...

    The fibronectin type III domain (FN3) has become one of the most widely used non-antibody scaffolds for generating new binding proteins. Because of its structural homology to the immunoglobulin domain, combinatorial libraries of FN3 designed to date have primarily focused on introducing amino acid diversity into three loops that are equivalent to antibody complementarity-determining regions. Here, we report an FN3 library that utilizes alternative positions for presenting amino acid diversity. We diversified positions on a β-sheet and surface loops that together form a concave surface. The new library produced binding proteins (termed "monobodies") to multiple target proteins, generally with similar efficacy as the original, loop-focused library. The crystal structure of a monobody generated from the new library in complex with its target, the Abl SH2 domain, revealed that a concave surface of the monobody, as intended in our design, bound to a convex surface of the target with the interface area being among the largest of published structures of monobody-target complexes. This mode of interaction differs from a common binding mode for single-domain antibodies and antibody mimics in which recognition loops recognize clefts in targets. Together, this work illustrates the utilization of different surfaces of a single immunoglobulin-like scaffold to generate binding proteins with distinct characteristics.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago,IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Monobody ySMB-9
A, B
95N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 1
C, D
99Homo sapiensMutation(s): 1 
Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens)
Go to Gene View: SUMO1
Go to UniProtKB:  P63165
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 93.347α = 90.00
b = 97.829β = 90.00
c = 96.578γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MD2data collection
MOLREPphasing
MAR345data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-05-23
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description