4V6D Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting date
authors Zhang, W., Dunkle, J.A., Cate, J.H.D.
compound source
symmetry
R_factor
R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.81
note 4V6D supersedes 3I1Q, 3I1R, 3I1S, 3I1T
Gene
Ontology
ChainFunctionProcessComponent
AB, CB


AC, CC


AH, CH


AI, CI


AL, CL


AM, CM


AN, CN


AO, CO
  • mRNA binding involved in pos...


  • AS, CS


    AT, CT
  • ornithine decarboxylase inhi...


  • AU, CU


    B0, D0


    B1, D1


    B3, D3


    B4, D4


    BC, DC


    BE, DE


    BF, DF


    BL, DL


    BN, DN


    BO, DO


    BQ, DQ
  • translation repressor activi...


  • BS, DS


    BT, DT


    BW, DW


    BX, DX


    BY, DY


    CD, AD


    CE, AE


    CF, AF


    CG, AG


    CJ, AJ


    CK, AK


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


  • CQ, AQ


    CR, AR


    D2, B2


    DD, BD


    DG, BG


    DH, BH


    DI, BI


    DJ, BJ


    DK, BK


    DM, BM


    DP, BP


    DR, BR


    DU, BU


    DV, BV


    DZ, BZ


    Primary referenceStructures of the ribosome in intermediate states of ratcheting., Zhang W, Dunkle JA, Cate JH, Science. 2009 Aug 21;325(5943):1014-7. PMID:19696352
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2211 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V6D
  • Structure Factors (3876 Kb)
  • Retrieve 4V6D in mmCIF format [Save to disk]
  • View 4V6D 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 4V6D
  • 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: [4v6d_DW] [4v6d_DG] [4v6d_AO] [4v6d_BV] [4v6d_CE] [4v6d_CF] [4v6d_CA] [4v6d_BB] [4v6d_BR] [4v6d_DR] [4v6d_B1] [4v6d_CG] [4v6d_AJ] [4v6d_DM] [4v6d_DS] [4v6d_BK] [4v6d_DF] [4v6d_CD] [4v6d_BJ] [4v6d_BT] [4v6d_D2] [4v6d] [4v6d_BS] [4v6d_DT] [4v6d_D1] [4v6d_CP] [4v6d_B4] [4v6d_DK] [4v6d_AA] [4v6d_DP] [4v6d_AC] [4v6d_DA] [4v6d_AW] [4v6d_DO] [4v6d_CC] [4v6d_DX] [4v6d_DU] [4v6d_DC] [4v6d_CJ] [4v6d_DI] [4v6d_B0] [4v6d_AS] [4v6d_CR] [4v6d_CS] [4v6d_BQ] [4v6d_CW] [4v6d_CT] [4v6d_BE] [4v6d_DQ] [4v6d_DZ] [4v6d_DY] [4v6d_AV] [4v6d_DL] [4v6d_CI] [4v6d_AQ] [4v6d_AN] [4v6d_CV] [4v6d_CM] [4v6d_BO] [4v6d_AI] [4v6d_BW] [4v6d_AL] [4v6d_DJ] [4v6d_CL] [4v6d_BH] [4v6d_AT] [4v6d_BL] [4v6d_B2] [4v6d_AP] [4v6d_BM] [4v6d_BF] [4v6d_DV] [4v6d_BU] [4v6d_CB] [4v6d_AR] [4v6d_BD] [4v6d_AD] [4v6d_BX] [4v6d_AK] [4v6d_AE] [4v6d_DB] [4v6d_CQ] [4v6d_BZ] [4v6d_BP] [4v6d_AG] [4v6d_AU] [4v6d_D0] [4v6d_BI] [4v6d_BA] [4v6d_DN] [4v6d_CH] [4v6d_BC] [4v6d_BN] [4v6d_BY] [4v6d_DE] [4v6d_AF] [4v6d_CN] [4v6d_CU] [4v6d_AH] [4v6d_D3] [4v6d_DH] [4v6d_CK] [4v6d_CO] [4v6d_AM] [4v6d_DD] [4v6d_D4] [4v6d_AB] [4v6d_B3] [4v6d_BG]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V6D: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4V6D
  • Community annotation for 4V6D at PDBWiki (http://pdbwiki.org)

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