4A3E RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP date
authors Cheung, A.C.M., Sainsbury, S., Cramer, P.
compound source
symmetry
R_factor
R_Free 0.1878
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.40
ligand APC, BRU, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


  • B
  • RNA-directed 5'-3' RNA polym...


  • C
  • RNA-directed 5'-3' RNA polym...


  • D
  • RNA-directed 5'-3' RNA polym...


  • E
  • RNA-directed 5'-3' RNA polym...


  • F
  • RNA-directed 5'-3' RNA polym...


  • G
  • RNA-directed 5'-3' RNA polym...


  • H
  • RNA-directed 5'-3' RNA polym...


  • I
  • RNA-directed 5'-3' RNA polym...


  • J
  • RNA-directed 5'-3' RNA polym...

  • DNA-directed RNA polymerase ...
  • K
  • RNA-directed 5'-3' RNA polym...


  • L
  • RNA-directed 5'-3' RNA polym...


  • Primary referenceStructural basis of initial RNA polymerase II transcription., Cheung AC, Sainsbury S, Cramer P, EMBO J. 2011 Nov 4. doi: 10.1038/emboj.2011.396. PMID:22056778
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1377 Kb) [Save to disk]
  • Biological Unit Coordinates (4a3e.pdb1.gz) 1361 Kb
  • LPC: Ligand-Protein Contacts for 4A3E
  • CSU: Contacts of Structural Units for 4A3E
  • Structure Factors (2212 Kb)
  • Retrieve 4A3E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A3E from S2C, [Save to disk]
  • Re-refined 4a3e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A3E 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 4A3E
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4A3E, from MSDmotif at EBI
  • Fold representative 4a3e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a3e_D] [4a3e_C] [4a3e_K] [4a3e_L] [4a3e_G] [4a3e_B] [4a3e_P] [4a3e_I] [4a3e_T] [4a3e_E] [4a3e_F] [4a3e_N] [4a3e] [4a3e_A] [4a3e_H] [4a3e_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4A3E: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 4A3E
  • Community annotation for 4A3E at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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