4V4V Structure of a pre-translocational E. coli ribosome obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1056 date
authors Mitra, K., Frank, J.
compound source
symmetry
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 15.00
note 4V4V supersedes 2GY9, 2GYA
Gene
Ontology
ChainFunctionProcessComponent
AB


AC


AD


AE


AF


AG


AH


AI


AJ


AK


AL


AM


AN


AO
  • mRNA binding involved in pos...


  • AP
  • nuclease activity
  • endonuclease activity
  • endodeoxyribonuclease activi...


  • AQ


    AR


    AS


    AT
  • ornithine decarboxylase inhi...


  • B1


    B2


    B5, B3


    BA


    BB


    BC


    BD


    BE


    BF


    BG


    BH


    BI


    BJ


    BK


    BL


    BM


    BN


    BO
  • translation repressor activi...


  • BQ


    BR


    BS


    BT


    BU


    BW


    BX


    BZ


    Primary referenceElongation arrest by SecM via a cascade of ribosomal RNA rearrangements., Mitra K, Schaffitzel C, Fabiola F, Chapman MS, Ban N, Frank J, Mol Cell. 2006 May 19;22(4):533-43. PMID:16713583
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (915 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V4V
  • Retrieve 4V4V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V4V from S2C, [Save to disk]
  • View 4V4V 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 4V4V
  • 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: [4v4v_AK] [4v4v_BF] [4v4v_AP] [4v4v_BC] [4v4v_BN] [4v4v_AT] [4v4v_BK] [4v4v_B9] [4v4v_BZ] [4v4v_AH] [4v4v_BS] [4v4v_BQ] [4v4v_AI] [4v4v_B5] [4v4v_BD] [4v4v_AG] [4v4v_BT] [4v4v_B0] [4v4v_AV] [4v4v_B3] [4v4v_BR] [4v4v_B2] [4v4v_AW] [4v4v_BL] [4v4v_BB] [4v4v_AC] [4v4v_BG] [4v4v_AM] [4v4v_AJ] [4v4v_AS] [4v4v_BE] [4v4v_BX] [4v4v_AN] [4v4v_AA] [4v4v_AQ] [4v4v_AL] [4v4v_BW] [4v4v_BM] [4v4v_AE] [4v4v_BO] [4v4v_AD] [4v4v_BJ] [4v4v_AU] [4v4v_BU] [4v4v_AR] [4v4v_AO] [4v4v_BH] [4v4v_AB] [4v4v_BI] [4v4v_BA] [4v4v_AF] [4v4v] [4v4v_B1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V4V: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4V4V
  • Community annotation for 4V4V at PDBWiki (http://pdbwiki.org)

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