4IFD Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA date
authors Makino, D.L., Conti, E.
compound source
symmetry
R_factor
R_Free 0.2239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.81
ligand BR, GOL, MES, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • B

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • C

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • D

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • E

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • F

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • G

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • H

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • I

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • J
  • endoribonuclease activity

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • Primary referenceCrystal structure of an RNA-bound 11-subunit eukaryotic exosome complex., Makino DL, Baumgartner M, Conti E, Nature. 2013 Mar 7;495(7439):70-5. doi: 10.1038/nature11870. Epub 2013 Feb 3. PMID:23376952
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1093 Kb) [Save to disk]
  • Biological Unit Coordinates (4ifd.pdb1.gz) 1081 Kb
  • LPC: Ligand-Protein Contacts for 4IFD
  • CSU: Contacts of Structural Units for 4IFD
  • Structure Factors (1884 Kb)
  • Retrieve 4IFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IFD from S2C, [Save to disk]
  • Re-refined 4ifd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IFD 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 4IFD
  • 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 4IFD, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ifd_C] [4ifd_R] [4ifd_I] [4ifd] [4ifd_F] [4ifd_D] [4ifd_G] [4ifd_A] [4ifd_B] [4ifd_H] [4ifd_J] [4ifd_K] [4ifd_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4IFD: [PINc] [RNB] [S1 ] by SMART
  • Other resources with information on 4IFD
  • Community annotation for 4IFD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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