4D61 Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state date
authors Muhs, M., Hilal, T., Mielke, T., Skabkin, M.A., Sanbonmatsu, K.Y., Pestova, T.V., Spahn, C.M.T.
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symmetry
R_factor
R_Free
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length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 9.00
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Primary referenceCryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES., Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CM, Mol Cell. 2015 Feb 5;57(3):422-432. doi: 10.1016/j.molcel.2014.12.016. Epub 2015 , Jan 15. PMID:25601755
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1500 Kb) [Save to disk]
  • Biological Unit Coordinates (4d61.pdb1.gz) 1486 Kb
  • CSU: Contacts of Structural Units for 4D61
  • Retrieve 4D61 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D61 from S2C, [Save to disk]
  • View 4D61 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 4D61
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4D61, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d61_A] [4d61_i] [4d61_T] [4d61_C] [4d61_M] [4d61_D] [4d61_J] [4d61_O] [4d61_I] [4d61_W] [4d61_S] [4d61_g] [4d61_f] [4d61_F] [4d61_e] [4d61] [4d61_h] [4d61_j] [4d61_b] [4d61_X] [4d61_c] [4d61_d] [4d61_1] [4d61_H] [4d61_E] [4d61_Y] [4d61_R] [4d61_Q] [4d61_P] [4d61_N] [4d61_V] [4d61_U] [4d61_G] [4d61_Z] [4d61_a] [4d61_K] [4d61_L] [4d61_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4D61: [KH] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [UBQ] [WD40] [eRF1_1 ] by SMART
  • Other resources with information on 4D61
  • Community annotation for 4D61 at PDBWiki (http://pdbwiki.org)

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