4V50 Crystal Structure of Ribosome with messenger RNA and the Anticodon stem-loop of P-site tRNA. date
authors Berk, V., Zhang, W., Pai, R.D., Cate, J.H.D.
compound source
symmetry
R_factor
R_Free 0.32
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.22
note 4V50 supersedes 2I2P, 2I2T, 2I2U, 2I2V
Gene
Ontology
ChainFunctionProcessComponent
AB, CB


AC, CC


AH, CH


AI, CI


AL, CL


AM, CM


AN, CN


AO, CO


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 referenceStructural basis for mRNA and tRNA positioning on the ribosome., Berk V, Zhang W, Pai RD, Cate JH, Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15830-4. Epub 2006 Oct 12. PMID:17038497
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (967 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 4V50
  • Structure Factors (6918 Kb)
  • Retrieve 4V50 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V50 from S2C, [Save to disk]
    • View 4V50 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 4V50
  • 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: [4v50_BY] [4v50_BG] [4v50_CA] [4v50_AG] [4v50_CQ] [4v50_CF] [4v50_BB] [4v50_BD] [4v50_DZ] [4v50_BL] [4v50_AO] [4v50_BK] [4v50_AP] [4v50_DS] [4v50_AU] [4v50_BE] [4v50_AD] [4v50_AX] [4v50_DK] [4v50_BC] [4v50_AJ] [4v50_B1] [4v50_AK] [4v50_BW] [4v50_DX] [4v50_BV] [4v50_CK] [4v50_CD] [4v50_AQ] [4v50_AT] [4v50_AE] [4v50_B0] [4v50_CS] [4v50_DE] [4v50_D4] [4v50_CP] [4v50_BR] [4v50_CI] [4v50_DR] [4v50_B3] [4v50_DQ] [4v50_BT] [4v50_AB] [4v50_D3] [4v50_D2] [4v50_AL] [4v50_CH] [4v50_DJ] [4v50_DN] [4v50_DU] [4v50_AS] [4v50_DI] [4v50_DD] [4v50_BM] [4v50_D1] [4v50_CJ] [4v50_BI] [4v50_AM] [4v50] [4v50_BS] [4v50_BQ] [4v50_AC] [4v50_DC] [4v50_CU] [4v50_BA] [4v50_CB] [4v50_B2] [4v50_CE] [4v50_BX] [4v50_DV] [4v50_DO] [4v50_DH] [4v50_BN] [4v50_DL] [4v50_CR] [4v50_DG] [4v50_CC] [4v50_AF] [4v50_DW] [4v50_AR] [4v50_BH] [4v50_BP] [4v50_B4] [4v50_BU] [4v50_BF] [4v50_BZ] [4v50_CT] [4v50_CG] [4v50_CL] [4v50_AN] [4v50_BO] [4v50_AI] [4v50_CX] [4v50_CW] [4v50_DY] [4v50_DB] [4v50_CN] [4v50_D0] [4v50_BJ] [4v50_AH] [4v50_DF] [4v50_AW] [4v50_DT] [4v50_DP] [4v50_CM] [4v50_CO] [4v50_AA] [4v50_DA] [4v50_DM]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V50: [KH] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4V50
  • Community annotation for 4V50 at PDBWiki (http://pdbwiki.org)

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