4YLO E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA date
authors Zuo, Y., Steitz, T.A.
compound source
symmetry
R_factor
R_Free 0.31429
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 6.00
ligand GTP, MG, ZN enzyme
Gene ECE24377A ; ECE24377A ; ECE24377A ; ECE24377A
Gene
Ontology
ChainFunctionProcessComponent
C, O, I


F, L, R
  • bacterial sigma factor activ...


    • J, P, D


    K, E, Q


    N, M, A, B, H, G


    Primary referenceCrystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble., Zuo Y, Steitz TA, Mol Cell. 2015 Apr 8. pii: S1097-2765(15)00175-6. doi:, 10.1016/j.molcel.2015.03.010. PMID:25866247
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (4174 Kb) [Save to disk]
  • Biological Unit Coordinates (4ylo.pdb1.gz) 1404 Kb
  • Biological Unit Coordinates (4ylo.pdb2.gz) 1400 Kb
  • Biological Unit Coordinates (4ylo.pdb3.gz) 1400 Kb
  • LPC: Ligand-Protein Contacts for 4YLO
  • CSU: Contacts of Structural Units for 4YLO
  • Structure Factors (1040 Kb)
  • Retrieve 4YLO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YLO from S2C, [Save to disk]
  • Re-refined 4ylo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YLO 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 4YLO
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4YLO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ylo_A] [4ylo_F] [4ylo_Q] [4ylo_N] [4ylo_J] [4ylo_5] [4ylo_I] [4ylo_4] [4ylo_D] [4ylo_G] [4ylo_P] [4ylo_M] [4ylo_3] [4ylo_6] [4ylo_K] [4ylo_B] [4ylo_2] [4ylo_O] [4ylo_9] [4ylo_C] [4ylo_8] [4ylo_7] [4ylo_H] [4ylo] [4ylo_E] [4ylo_R] [4ylo_L] [4ylo_1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YLO: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
    • Other resources with information on 4YLO
  • Community annotation for 4YLO at PDBWiki (http://pdbwiki.org)

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