Solution NMR Structure of DE NOVO DESIGNED PROTEIN, IF3-like fold, Northeast Structural Genomics Consortium Target OR135 (CASD target)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


Principles for designing ideal protein structures.

Koga, N.Tatsumi-Koga, R.Liu, G.Xiao, R.Acton, T.B.Montelione, G.T.Baker, D.

(2012) Nature 491: 222-227

  • DOI: https://doi.org/10.1038/nature11600
  • Primary Citation of Related Structures:  
    2KL8, 2LN3, 2LTA, 2LV8, 2LVB

  • PubMed Abstract: 

    Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features--for example kinked α-helices, bulged β-strands, strained loops and buried polar groups--that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of α-helices, β-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.

  • Organizational Affiliation

    University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle, Washington 98195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DE NOVO DESIGNED PROTEIN OR13583synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-06-13
    Changes: Database references, Structure summary
  • Version 1.2: 2012-10-31
    Changes: Database references
  • Version 1.3: 2012-11-07
    Changes: Database references
  • Version 1.4: 2013-01-23
    Changes: Database references
  • Version 1.5: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.6: 2024-05-15
    Changes: Data collection, Database references