5IOO

Accommodation of massive sequence variation in Nanoarchaeota by the C-type lectin fold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements.

Handa, S.Paul, B.G.Miller, J.F.Valentine, D.L.Ghosh, P.

(2016) BMC Struct Biol 16: 13-13

  • DOI: https://doi.org/10.1186/s12900-016-0064-6
  • Primary Citation of Related Structures:  
    5IOO

  • PubMed Abstract: 

    Diversity-generating retroelements (DGRs) provide organisms with a unique means for adaptation to a dynamic environment through massive protein sequence variation. The potential scope of this variation exceeds that of the vertebrate adaptive immune system. DGRs were known to exist only in viruses and bacteria until their recent discovery in archaea belonging to the 'microbial dark matter', specifically in organisms closely related to Nanoarchaeota. However, Nanoarchaeota DGR variable proteins were unassignable to known protein folds and apparently unrelated to characterized DGR variable proteins.


  • Organizational Affiliation

    Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AvpA
A, B
255Nanoarchaeota archaeon JGI OTU-1Mutation(s): 0 
UniProt
Find proteins for A0A1L1QK08 (Nanoarchaeota archaeon JGI OTU-1)
Explore A0A1L1QK08 
Go to UniProtKB:  A0A1L1QK08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L1QK08
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.998α = 90
b = 143.998β = 90
c = 59.261γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI096838

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence