6QAZ | pdb_00006qaz

Crystal structure of gp41-1 intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 
    0.150 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.121 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 
    0.123 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6QAZ

This is version 1.3 of the entry. See complete history

Literature

The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from cis-splicing inteins.

Beyer, H.M.Mikula, K.M.Li, M.Wlodawer, A.Iwai, H.

(2020) FEBS J 287: 1886-1898

  • DOI: https://doi.org/10.1111/febs.15113
  • Primary Citation Related Structures: 
    6QAZ

  • PubMed Abstract: 

    Protein trans-splicing catalyzed by split inteins has increasingly become useful as a protein engineering tool. We solved the 1.0 Å-resolution crystal structure of a fused variant from the naturally split gp41-1 intein, previously identified from environmental metagenomic sequence data. The structure of the 125-residue gp41-1 intein revealed a compact pseudo-C2-symmetry commonly found in the Hedgehog/Intein superfamily with extensive charge-charge interactions between the split N- and C-terminal intein fragments that are common among naturally occurring split inteins. We successfully created orthogonal split inteins by engineering a similar charge network into the same region of a cis-splicing intein. This strategy could be applicable for creating novel natural-like split inteins from other, more prevalent cis-splicing inteins. DATABASE: Structural data are available in the RCSB Protein Data Bank under the accession number 6QAZ.


  • Organizational Affiliation
    • Research Program in Structural Biology and Biophysics, Helsinki Life Science Institute-Institute of Biotechnology, University of Helsinki, Finland.

Macromolecule Content 

  • Total Structure Weight: 15.23 kDa 
  • Atom Count: 1,364 
  • Modeled Residue Count: 128 
  • Deposited Residue Count: 128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cyanophage-like gp41-1 intein128metagenomeMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free:  0.150 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.121 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 0.123 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.809α = 90
b = 69.986β = 90
c = 71.236γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland137995, 277335
Novo Nordisk FoundationFinlandNNF17OC0025402
Sigrid Juselius FoundationFinland--
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHHSN261200800001E

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description