7DMF

A de novo protein that rigidly extends the structure of tVHS-like domain in tepsin with a new designed domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A backbone-centred energy function of neural networks for protein design.

Huang, B.Xu, Y.Hu, X.Liu, Y.Liao, S.Zhang, J.Huang, C.Hong, J.Chen, Q.Liu, H.

(2022) Nature 602: 523-528

  • DOI: https://doi.org/10.1038/s41586-021-04383-5

  • PubMed Abstract: 

    A protein backbone structure is designable if a substantial number of amino acid sequences exist that autonomously fold into it 1,2 . It has been suggested that the designability of backbones is governed mainly by side chain-independent or side chain type-insensitive molecular interactions 3-5 , indicating an approach for designing new backbones (ready for amino acid selection) based on continuous sampling and optimization of the backbone-centred energy surface. However, a sufficiently comprehensive and precise energy function has yet to be established for this purpose. Here we show that this goal is met by a statistical model named SCUBA (for Side Chain-Unknown Backbone Arrangement) that uses neural network-form energy terms. These terms are learned with a two-step approach that comprises kernel density estimation followed by neural network training and can analytically represent multidimensional, high-order correlations in known protein structures. We report the crystal structures of nine de novo proteins whose backbones were designed to high precision using SCUBA, four of which have novel, non-natural overall architectures. By eschewing use of fragments from existing protein structures, SCUBA-driven structure design facilitates far-reaching exploration of the designable backbone space, thus extending the novelty and diversity of the proteins amenable to de novo design.


  • Organizational Affiliation

    MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Designed protein EXTD-3189synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.727α = 90
b = 69.727β = 90
c = 79.291γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2021-12-08 
  • Deposition Author(s): Xu, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references, Structure summary
  • Version 1.2: 2022-02-23
    Changes: Database references, Structure summary
  • Version 1.3: 2022-03-02
    Changes: Database references
  • Version 1.4: 2022-03-09
    Changes: Refinement description
  • Version 1.5: 2023-11-29
    Changes: Data collection, Refinement description