6R5Y

8-bladed beta-propeller formed by two 4-bladed fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural diversity of oligomeric beta-propellers with different numbers of identical blades.

Afanasieva, E.Chaudhuri, I.Martin, J.Hertle, E.Ursinus, A.Alva, V.Hartmann, M.D.Lupas, A.N.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.49853
  • Primary Citation of Related Structures:  
    6R5X, 6R5Y, 6R5Z, 6R60

  • PubMed Abstract: 

    β-Propellers arise through the amplification of a supersecondary structure element called a blade. This process produces toroids of between four and twelve repeats, which are almost always arranged sequentially in a single polypeptide chain. We found that new propellers evolve continuously by amplification from single blades. We therefore investigated whether such nascent propellers can fold as homo-oligomers before they have been fully amplified within a single chain. One- to six-bladed building blocks derived from two seven-bladed WD40 propellers yielded stable homo-oligomers with six to nine blades, depending on the size of the building block. High-resolution structures for tetramers of two blades, trimers of three blades, and dimers of four and five blades, respectively, show structurally diverse propellers and include a novel fold, highlighting the inherent flexibility of the WD40 blade. Our data support the hypothesis that subdomain-sized fragments can provide structural versatility in the evolution of new proteins.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD-40 repeat protein
A, B, C, D, E
A, B, C, D, E, F
168Nostoc punctiformeMutation(s): 0 
Gene Names: Npun_R6612
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.721α = 90
b = 127.167β = 90
c = 72.958γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description