Structural basis for assembly and function of the Nup82 complex in the nuclear pore scaffold

The yeast Nup82 complex forms an unusual asymmetric structure with a dimeric array of subunits that mediate its anchorage to the NPC scaffold and its concomitant interaction with the soluble nucleocytoplasmic transport machinery.

[1]  B. Böttcher,et al.  Reconstitution of Nup157 and Nup145N into the Nup84 Complex*[boxs] , 2005, Journal of Biological Chemistry.

[2]  Helen Pickersgill,et al.  Nup358/RanBP2 Attaches to the Nuclear Pore Complex via Association with Nup88 and Nup214/CAN and Plays a Supporting Role in CRM1-Mediated Nuclear Protein Export , 2004, Molecular and Cellular Biology.

[3]  Jerry H. Brown.  How sequence directs bending in tropomyosin and other two‐stranded alpha‐helical coiled coils , 2010, Protein science : a publication of the Protein Society.

[4]  A. Hoelz,et al.  Molecular basis for the anchoring of proto-oncoprotein Nup98 to the cytoplasmic face of the nuclear pore complex. , 2012, Journal of molecular biology.

[5]  S. R. Wente,et al.  The DEAD-box protein Dbp5 controls mRNA export by triggering specific RNA:protein remodeling events. , 2007, Molecular cell.

[6]  P. Philippsen,et al.  Molecular basis for the functional interaction of dynein light chain with the nuclear-pore complex , 2007, Nature Cell Biology.

[7]  P. Grandi,et al.  A novel nuclear pore protein Nup82p which specifically binds to a fraction of Nsp1p , 1995, The Journal of cell biology.

[8]  B. Chait,et al.  The Yeast Nuclear Pore Complex: Composition, Architecture, and Transport Mechanism , 2000 .

[9]  Friedrich Förster,et al.  False discovery rate estimation for cross-linked peptides identified by mass spectrometry , 2012, Nature Methods.

[10]  Brendan MacLean,et al.  Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .

[11]  M. Beck,et al.  The use of targeted proteomics to determine the stoichiometry of large macromolecular assemblies. , 2014, Methods in cell biology.

[12]  J. Philo.  Improved methods for fitting sedimentation coefficient distributions derived by time-derivative techniques. , 2006, Analytical biochemistry.

[13]  C. Cole,et al.  A conditional allele of the novel repeat-containing yeast nucleoporin RAT7/NUP159 causes both rapid cessation of mRNA export and reversible clustering of nuclear pore complexes , 1995, The Journal of cell biology.

[14]  S. Bailer,et al.  The Nsp1p Carboxy-Terminal Domain Is Organized into Functionally Distinct Coiled-Coil Regions Required for Assembly of Nucleoporin Subcomplexes and Nucleocytoplasmic Transport , 2001, Molecular and Cellular Biology.

[15]  André Hoelz,et al.  Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex , 2011, Proceedings of the National Academy of Sciences.

[16]  J. García de la Torre,et al.  HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images , 2001, European Biophysics Journal.

[17]  C. Dominguez,et al.  HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.

[18]  Alexandre M J J Bonvin,et al.  Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. , 2010, Journal of proteome research.

[19]  Yang Zhang,et al.  I-TASSER server for protein 3D structure prediction , 2008, BMC Bioinformatics.

[20]  E. Barbar.  Dynein light chain LC8 is a dimerization hub essential in diverse protein networks. , 2008, Biochemistry.

[21]  A. Bonvin,et al.  The HADDOCK web server for data-driven biomolecular docking , 2010, Nature Protocols.

[22]  Ralf P. Richter,et al.  FG-Rich Repeats of Nuclear Pore Proteins Form a Three-Dimensional Meshwork with Hydrogel-Like Properties , 2006, Science.

[23]  G. Blobel,et al.  The Essential Yeast Nucleoporin NUP159 Is Located on the Cytoplasmic Side of the Nuclear Pore Complex and Serves in Karyopherin-mediated Binding of Transport Substrate (*) , 1995, The Journal of Biological Chemistry.

[24]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[25]  C. Cole,et al.  Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1‐1 cells , 1999, The EMBO journal.

[26]  J. Berger,et al.  A conserved mechanism of DEAD-box ATPase activation by nucleoporins and IP6 in mRNA export , 2011, Nature.

[27]  David Tollervey,et al.  60S pre‐ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm , 2002, The EMBO journal.

[28]  E. Hurt,et al.  Monitoring spatiotemporal biogenesis of macromolecular assemblies by pulse-chase epitope labeling. , 2012, Molecular cell.

[29]  K. Thompson,et al.  Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4. , 1993, Biochemistry.

[30]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[31]  E. Barbar,et al.  Light Chain-dependent Self-association of Dynein Intermediate Chain* , 2010, The Journal of Biological Chemistry.

[32]  P. Bork,et al.  Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines , 2013, Molecular systems biology.

[33]  A. Brunger.  Version 1.2 of the Crystallography and NMR system , 2007, Nature Protocols.

[34]  U. Aebi,et al.  Nanomechanical Basis of Selective Gating by the Nuclear Pore Complex , 2007, Science.

[35]  M. Beck,et al.  Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold , 2013, Cell.

[36]  J. Berger,et al.  The N-terminal domain of Nup159 forms a beta-propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore. , 2004, Molecular cell.

[37]  C. Cole,et al.  Functional characterization of a Nup159p-containing nuclear pore subcomplex. , 1998, Molecular biology of the cell.

[38]  E. Hurt,et al.  Gene regulation by nucleoporins and links to cancer. , 2010, Molecular cell.

[39]  Henning Urlaub,et al.  GraFix: sample preparation for single-particle electron cryomicroscopy , 2008, Nature Methods.

[40]  C. Cole,et al.  The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1. , 2011, Genes & development.

[41]  R. Abagyan,et al.  Identification of protein-protein interaction sites from docking energy landscapes. , 2004, Journal of molecular biology.

[42]  L. S. Swapna,et al.  Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance , 2012, PloS one.

[43]  R. Wozniak,et al.  Inheritance of yeast nuclear pore complexes requires the Nsp1p subcomplex , 2013, The Journal of cell biology.

[44]  Christian Cole,et al.  The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..

[45]  C. Cole,et al.  A structure/function analysis of Rat7p/Nup159p, an essential nucleoporin of Saccharomyces cerevisiae. , 1997, Journal of cell science.

[46]  A Leith,et al.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. , 1996, Journal of structural biology.

[47]  M van Heel,et al.  A new generation of the IMAGIC image processing system. , 1996, Journal of structural biology.

[48]  Marieke,et al.  Can, a putative oncogene associated with myeloid leukemogenesis, may be activated by fusion of its 3' half to different genes: characterization of the set gene , 1992, Molecular and cellular biology.

[49]  Yang Zhang,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[50]  P. Kastritis,et al.  On the binding affinity of macromolecular interactions: daring to ask why proteins interact , 2013, Journal of The Royal Society Interface.

[51]  G. Blobel,et al.  NUP82 is an essential yeast nucleoporin required for poly(A)+ RNA export , 1995, The Journal of cell biology.

[52]  F. Melchior,et al.  RanGTP targets p97 to RanBP2, a filamentous protein localized at the cytoplasmic periphery of the nuclear pore complex. , 1997, Molecular biology of the cell.

[53]  G. Blobel,et al.  Crystal structure of the N-terminal domain of the human protooncogene Nup214/CAN , 2007, Proceedings of the National Academy of Sciences.

[54]  B. Séraphin,et al.  Dbp5, a DEAD‐box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p , 1999, The EMBO journal.

[55]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[56]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[57]  M. Beck,et al.  Protein interfaces of the conserved Nup84 complex from Chaetomium thermophilum shown by crosslinking mass spectrometry and electron microscopy. , 2013, Structure.

[58]  M. Mann,et al.  Nup116p Associates with the Nup82p-Nsp1p-Nup159p Nucleoporin Complex* , 2000, The Journal of Biological Chemistry.

[59]  E. Hurt,et al.  A novel nucleoskeletal‐like protein located at the nuclear periphery is required for the life cycle of Saccharomyces cerevisiae. , 1988, The EMBO journal.

[60]  P. Grandi,et al.  Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p. , 1995, The EMBO journal.

[61]  W Chiu,et al.  EMAN: semiautomated software for high-resolution single-particle reconstructions. , 1999, Journal of structural biology.

[62]  G. Blobel,et al.  The human CAN protein, a putative oncogene product associated with myeloid leukemogenesis, is a nuclear pore complex protein that faces the cytoplasm. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[63]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[64]  G. Grosveld,et al.  G2 arrest and impaired nucleocytoplasmic transport in mouse embryos lacking the proto‐oncogene CAN/Nup214. , 1996, The EMBO journal.

[65]  R. Aebersold,et al.  Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography , 2012, Molecular & Cellular Proteomics.

[66]  F. Förster,et al.  Nuclear Pore Complex Structure and Dynamics Revealed by Cryoelectron Tomography , 2004, Science.

[67]  M. Moragues,et al.  The nuclear pore complex protein Nup88 is overexpressed in tumor cells. , 1999, Cancer research.

[68]  T. Surrey,et al.  Reconstitution of the human cytoplasmic dynein complex , 2012, Proceedings of the National Academy of Sciences.

[69]  E. Hurt,et al.  The NUG1 GTPase Reveals an N-terminal RNA-binding Domain That Is Essential for Association with 60 S Pre-ribosomal Particles* , 2006, Journal of Biological Chemistry.

[70]  Alexandre M J J Bonvin,et al.  Molecular origins of binding affinity: seeking the Archimedean point. , 2013, Current opinion in structural biology.

[71]  W. Stafford,et al.  Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. , 1992, Analytical biochemistry.

[72]  M. Fornerod,et al.  The human homologue of yeast CRM1 is in a dynamic subcomplex with CAN/Nup214 and a novel nuclear pore component Nup88 , 1997, The EMBO journal.

[73]  David N Mastronarde,et al.  Automated electron microscope tomography using robust prediction of specimen movements. , 2005, Journal of structural biology.

[74]  P. S. Kim,et al.  A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. , 1993, Science.

[75]  Alexandre M J J Bonvin,et al.  HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets , 2007, Proteins.

[76]  Ueli Aebi,et al.  The nuclear pore complex: nucleocytoplasmic transport and beyond , 2003, Nature Reviews Molecular Cell Biology.

[77]  E. Hurt,et al.  From nucleoporins to nuclear pore complexes. , 1997, Current opinion in cell biology.

[78]  H. Horstmann,et al.  NSP1: A yeast nuclear envelope protein localized at the nuclear pores exerts its essential function by its carboxy-terminal domain , 1990, Cell.