3F7F Structural Protein date Nov 08, 2008
title Structure Of Nup120
authors H.S.Seo, Y.Ma, E.W.Debler, G.Blobel, A.Hoelz
compound source
Molecule: Nucleoporin Nup120
Chain: A, B, C, D
Fragment: Unp Residues 1-729
Synonym: Nuclear Pore Protein Nup120
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
Gene: Nup120, Rat2, Ykl057c, Ykl314, Ykl313
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t1
symmetry Space Group: P 1
R_factor 0.232 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.680 117.478 146.287 89.94 89.77 89.89
method X-Ray Diffractionresolution 2.60 Å
ligand HG enzyme
Primary referenceStructural and functional analysis of Nup120 suggests ring formation of the Nup84 complex., Seo HS, Ma Y, Debler EW, Wacker D, Kutik S, Blobel G, Hoelz A, Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14281-6. Epub 2009 Aug 11. PMID:19706512
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (455 Kb) [Save to disk]
  • Biological Unit Coordinates (3f7f.pdb1.gz) 117 Kb
  • Biological Unit Coordinates (3f7f.pdb2.gz) 117 Kb
  • Biological Unit Coordinates (3f7f.pdb3.gz) 117 Kb
  • Biological Unit Coordinates (3f7f.pdb4.gz) 116 Kb
  • Biological Unit Coordinates (3f7f.pdb5.gz) 228 Kb
  • Biological Unit Coordinates (3f7f.pdb6.gz) 229 Kb
  • LPC: Ligand-Protein Contacts for 3F7F
  • CSU: Contacts of Structural Units for 3F7F
  • Structure Factors (2458 Kb)
  • Retrieve 3F7F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F7F from S2C, [Save to disk]
  • Re-refined 3f7f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F7F in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3F7F
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3F7F, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f7f_D] [3f7f_B] [3f7f_A] [3f7f_C] [3f7f]
  • SWISS-PROT database: [P35729]
  • Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB.
  • Domain organization of [NU120_YEAST] by SWISSPFAM
  • Other resources with information on 3F7F
  • Community annotation for 3F7F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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