Crystal structure of novel repeat protein BRIC2 fused to DARPin D12

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture.

ElGamacy, M.Coles, M.Ernst, P.Zhu, H.Hartmann, M.D.Pluckthun, A.Lupas, A.N.

(2018) ACS Synth Biol 7: 2226-2235

  • DOI: https://doi.org/10.1021/acssynbio.8b00224
  • Primary Citation of Related Structures:  
    6FES, 6FF6

  • PubMed Abstract: 

    Designing proteins with novel folds remains a major challenge, as the biophysical properties of the target fold are not known a priori and no sequence profile exists to describe its features. Therefore, most computational design efforts so far have been directed toward creating proteins that recapitulate existing folds. Here we present a strategy centered upon the design of novel intramolecular interfaces that enables the construction of a target fold from a set of starting fragments. This strategy effectively reduces the amount of computational sampling necessary to achieve an optimal sequence, without compromising the level of topological control. The solenoid architecture has been a target of extensive protein design efforts, as it provides a highly modular platform of low topological complexity. However, none of the previous efforts have attempted to depart from the natural form, which is characterized by a uniformly handed superhelical architecture. Here we aimed to design a more complex platform, abolishing the superhelicity by introducing internally alternating handedness, resulting in a novel, corrugated architecture. We employed our interface-driven strategy, designing three proteins and confirming the design by solving the structure of two examples.

  • Organizational Affiliation

    Department of Protein Evolution , Max-Planck-Institute for Developmental Biology , 72076 Tübingen , Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D12_BRIC2, a synthetic protein,D12_BRIC2, a synthetic protein
A, B, C, D
367synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
M [auth C],
P [auth D],
Q [auth D],
R [auth D]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
L [auth B]
N [auth C]
O [auth C]
H [auth A],
I [auth A],
L [auth B],
N [auth C],
O [auth C],
S [auth D],
T [auth D]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.99α = 97.99
b = 63β = 91.92
c = 133.54γ = 110.81
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description