4V4Y Crystal structure of the 70S Thermus thermophilus ribosome with translocated and rotated Shine-Dalgarno Duplex. date
authors Jenner, L., Yusupova, G., Rees, B., Moras, D., Yusupov, M.
compound source
symmetry
R_factor
R_Free 0.326
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 5.50
note 4V4Y supersedes 2HGP, 2HGQ
Gene
Ontology
ChainFunctionProcessComponent
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Primary referenceStructural basis for messenger RNA movement on the ribosome., Yusupova G, Jenner L, Rees B, Moras D, Yusupov M, Nature. 2006 Nov 16;444(7117):391-4. Epub 2006 Oct 18. PMID:17051149
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1134 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V4Y
  • Structure Factors (1875 Kb)
  • Retrieve 4V4Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V4Y from S2C, [Save to disk]
  • View 4V4Y 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 4V4Y
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4v4y_AW] [4v4y] [4v4y_AN] [4v4y_AX] [4v4y_BT] [4v4y_BA] [4v4y_AP] [4v4y_AG] [4v4y_BZ] [4v4y_AQ] [4v4y_BS] [4v4y_AS] [4v4y_AA] [4v4y_AJ] [4v4y_BC] [4v4y_BM] [4v4y_AD] [4v4y_BG] [4v4y_BW] [4v4y_AR] [4v4y_AH] [4v4y_B1] [4v4y_BF] [4v4y_AT] [4v4y_BH] [4v4y_B2] [4v4y_AB] [4v4y_AV] [4v4y_BL] [4v4y_AM] [4v4y_B4] [4v4y_BR] [4v4y_BO] [4v4y_B7] [4v4y_BD] [4v4y_BE] [4v4y_B5] [4v4y_BX] [4v4y_AE] [4v4y_AO] [4v4y_B8] [4v4y_BB] [4v4y_BV] [4v4y_BU] [4v4y_B6] [4v4y_AL] [4v4y_BP] [4v4y_A1] [4v4y_BQ] [4v4y_AC] [4v4y_AK] [4v4y_BN] [4v4y_AF] [4v4y_BY] [4v4y_B3] [4v4y_BK] [4v4y_AU] [4v4y_AI]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V4Y: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4V4Y
  • Community annotation for 4V4Y at PDBWiki (http://pdbwiki.org)

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