cryo-EM structure of ribonucleotide reductase from Synechococcus phage S-CBP4 bound with TTP

Experimental Data Snapshot

  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade.

Burnim, A.A.Spence, M.A.Xu, D.Jackson, C.J.Ando, N.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.79790
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from Synechococcus phage S-CBP4 and report the most minimal RNR architecture to-date. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleotide reductase
A, B
470Synechococcus phage S-CBP4Mutation(s): 0 
Gene Names: SVPG_00036
Find proteins for M1PRZ0 (Synechococcus phage S-CBP4)
Explore M1PRZ0 
Go to UniProtKB:  M1PRZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1PRZ0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1942668
National Science Foundation (NSF, United States)United StatesDMR-1719875

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2022-10-05
    Changes: Structure summary