Components of coated vesicles and nuclear pore complexes share a common molecular architecture

PLoS Biol. 2004 Dec;2(12):e380. doi: 10.1371/journal.pbio.0020380. Epub 2004 Nov 2.


Numerous features distinguish prokaryotes from eukaryotes, chief among which are the distinctive internal membrane systems of eukaryotic cells. These membrane systems form elaborate compartments and vesicular trafficking pathways, and sequester the chromatin within the nuclear envelope. The nuclear pore complex is the portal that specifically mediates macromolecular trafficking across the nuclear envelope. Although it is generally understood that these internal membrane systems evolved from specialized invaginations of the prokaryotic plasma membrane, it is not clear how the nuclear pore complex could have evolved from organisms with no analogous transport system. Here we use computational and biochemical methods to perform a structural analysis of the seven proteins comprising the yNup84/vNup107-160 subcomplex, a core building block of the nuclear pore complex. Our analysis indicates that all seven proteins contain either a beta-propeller fold, an alpha-solenoid fold, or a distinctive arrangement of both, revealing close similarities between the structures comprising the yNup84/vNup107-160 subcomplex and those comprising the major types of vesicle coating complexes that maintain vesicular trafficking pathways. These similarities suggest a common evolutionary origin for nuclear pore complexes and coated vesicles in an early membrane-curving module that led to the formation of the internal membrane systems in modern eukaryotes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Biochemistry / methods
  • Biological Transport
  • Cell Membrane / metabolism
  • Cell Nucleus / metabolism
  • Chromosome Mapping
  • Coated Vesicles / metabolism*
  • Computational Biology
  • Evolution, Molecular
  • Fungal Proteins / chemistry
  • Models, Biological
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Envelope / chemistry*
  • Nuclear Pore / metabolism
  • Nuclear Pore Complex Proteins / chemistry
  • Nuclear Pore Complex Proteins / physiology
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / physiology


  • Fungal Proteins
  • NUP133 protein, S cerevisiae
  • NUP84 protein, S cerevisiae
  • Nuclear Pore Complex Proteins
  • Saccharomyces cerevisiae Proteins

Associated data

  • SWISSPROT/P35729
  • SWISSPROT/P36161
  • SWISSPROT/P46673
  • SWISSPROT/P49687
  • SWISSPROT/P52891
  • SWISSPROT/P52948
  • SWISSPROT/P53011
  • SWISSPROT/P55735
  • SWISSPROT/P57740
  • SWISSPROT/Q04491
  • SWISSPROT/Q12769