3CAE

Structure of NNQQNY as an insert in T7 endonuclease I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.240 

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This is version 1.3 of the entry. See complete history


Literature

The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold.

Guo, Z.Eisenberg, D.

(2008) Protein Sci 17: 1617-1623

  • DOI: 10.1110/ps.036368.108
  • Primary Citation of Related Structures:  
    3CAE

  • PubMed Abstract: 
  • Numerous human disorders are associated with the formation of protein fibrils. The fibril-forming capacity of a protein has been found in recent studies to be determined by a short segment of residues that forms a dual beta-sheet, called a steric zipper, in the spine of the fibril ...

    Numerous human disorders are associated with the formation of protein fibrils. The fibril-forming capacity of a protein has been found in recent studies to be determined by a short segment of residues that forms a dual beta-sheet, called a steric zipper, in the spine of the fibril. The question arises as to whether a fibril-forming segment, when inserted within the sequence of a globular protein, will invariably cause the protein to form fibrils. Here we investigate this question by inserting the known fibril-forming segment NNQQNY into the globular enzyme, T7 endonuclease I. From earlier studies, we know that in its fibril form, NNQQNY is in an extended conformation. We first found that the inserted NNQQNY stimulates fibril formation of T7 endonuclease I in solution. Thus NNQQNY within T7 endonuclease I can exist in an extended conformation, capable of forming the steric zipper in the core of a fibril. We also found that T7 endonuclease I folds into a decamer that does not form fibrils. We determined the structure of the decamer by X-ray crystallography, finding an unusual oligomer without point group symmetry, and finding that the NNQQNY segments within the decamer adopt two twisted conformations, neither is apparently able to fibrillize. We conclude that twisting of fibril forming sequences from the fully extended conformation, imposed by the context of their placement in proteins, can interfere with fibril formation.


    Organizational Affiliation

    Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1570, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease IABCDEFGHABCDEFGHIJ
132Escherichia phage T7Mutation(s): 0 
Gene Names: 3
EC: 3.1.21.2
Find proteins for P00641 (Escherichia phage T7)
Explore P00641 
Go to UniProtKB:  P00641
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.408α = 90
b = 140.343β = 93.37
c = 88.508γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
BOSdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-02-19 
  • Released Date: 2008-07-22 
  • Deposition Author(s): Guo, Z., Eisenberg, D.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-06-07
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2017-10-25
    Changes: Refinement description