7BIE

Crystal structure of nvWrap-T, a 7-bladed symmetric propeller


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and stability of the designer protein WRAP-T and its permutants.

Mylemans, B.Lee, X.Y.Laier, I.Helsen, C.Voet, A.R.D.

(2021) Sci Rep 11: 18867-18867

  • DOI: https://doi.org/10.1038/s41598-021-98391-0
  • Primary Citation of Related Structures:  
    7BID, 7BIE, 7BIF, 7BIG

  • PubMed Abstract: 

    [Formula: see text]-Propeller proteins are common natural disc-like pseudo-symmetric proteins that contain multiple repeats ('blades') each consisting of a 4-stranded anti-parallel [Formula: see text]-sheet. So far, 4- to 12-bladed [Formula: see text]-propellers have been discovered in nature showing large functional and sequential variation. Using computational design approaches, we created perfectly symmetric [Formula: see text]-propellers out of natural pseudo-symmetric templates. These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. Here we describe such a engineered protein, based on a highly symmetric natural template, and test the effects of circular permutation on its stability. Geometrical analysis of this protein and other artificial symmetrical proteins reveals no systematic constraint that could be used to help in engineering of this fold, and suggests sequence constraints unique to each [Formula: see text]-propeller sub-family.


  • Organizational Affiliation

    Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
nvWRAP-T
A, B
329synthetic constructMutation(s): 9 
UniProt
Find proteins for B2J0I0 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2J0I0 
Go to UniProtKB:  B2J0I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2J0I0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
C [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.662α = 90
b = 48.497β = 101.47
c = 121.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0E4717N
Research Foundation - Flanders (FWO)BelgiumG0F9316N
Research Foundation - Flanders (FWO)BelgiumG051917N
Research Foundation - Flanders (FWO)BelgiumGBM-D3229-ASP/17

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description